TL;DR: I think the Luftwaffe crew will likely abort and attempt to get new orders, but if they don't it's going to go very badly for them.
First off, the German crews: Movies like Doctor Strangelove or How I Learned To Stop Worrying And Love The Bomb aside, most soldiers and fighter pilots are not in fact gung-ho slaughter-happy warmongers, and will in fact be hesitant to fire on a target that isn't what they're expecting without explicit orders.
On top of that, this is the height of the Blitz, meaning that at that point most of the Luftwaffe pilots that are still alive are the ones that learned to be cautious.
Even without instrumentation or radio contact, day or night, it's going to be incredibly obvious that something is very wrong. There should be a blackout (if at night) or at the very least radio silence, the Channel should be almost empty aside from destroyers looking for U-boats, as they reach visual range of the British coast there should be signs of battle damage...
... But the Channel is teeming with civilian ships, there are multiple harbors open along the coast, and even if they don't speak english the radio frequencies are full of voices that sound, at most, mildly curious about something.
The closer they get to their supposed target, the less sense anything makes. Who knows, maybe they are the mental equivalent of General Ripper or Major T. J. "King" Kong and they'll decide zum Teufel mit alles and bomb anyway, but I doubt it.
If they do, however, continue on to...
The British response
For the sake of brevity I'm going to assume that they appear within nominal British airspace, or close enough to it that the French wouldn't be able to intercept before they get there and diplomatic concerns mean they won't try until it's too late to do anything about it.
The entire British coast, and especially the Channel, is blanketed with ATC radar. It takes approximately 0.5 seconds for every ATC officer and pilot on duty to spot them, one second to blink in surprise, call it ten more seconds to verify that yes, that's an actual contact, no, they weren't there ten seconds before, no, ATC radar hasn't just spectacularly malfunctioned, so yes, there are 125 unidentified aircraft flying in formation on a course that takes them straight through every single traffic lane and right over London.
Civilian Air Traffic Control is highly organized and every single pilot and operator knows how it works. Pilots in at-risk approach vectors are alerted, and the designated operator for the new contact starts calling them to please identify and state your flight plan, repeating the call with increasing insistence and urgency and reminding them of the various penalties and problems.
(If any of the Luftwaffe pilots speaks English at all, this highly amplifies the was-zum-Teufel feeling they're already experiencing)
Military ATC is equally on the ball, although the ATC officer is going to have to explain that no, he wasn't sleeping on the job, those contacts just appeared well within radar range, at a speed at which they couldn't possibly have failed to be noticed earlier.
By modern standards, their speed is ridiculously slow and that formation has almost no practical use -- but enough officers are military history buffs that someone will recognize it as a standard Luftwaffe attack formation, which means that at a minimum someone with the resources to refurbish 125 WW2-era aircraft to operational status has decided to use those resources to play Silly Buggers.
The two on-the-deck craft scramble immediately, all other craft which can get into the air within the expected timespan goes through emergency prep-and-scramble, every anti-air system with a firing arc that'll reach gets put on alert, and civilian traffic is ordered to divert to other airports while they sort out what's going on. At this point a large number of important people have just had their day disturbed, everyone is more than a little irked.
The Typhoons' first flyby happens at close to their maximum speed and blows past the Geschwader at a speed the Luftwaffe can't even begin to comprehend, there and gone before any of the fighter pilots can even react.
On their return pass, coming from behind, they casually reduce speed to sidle up to one of the fighters so that they can see cockpit-to-cockpit and gesture at them to Land, Right Now, Because You Assholes Are In So Much Trouble Already It's Not Funny.
The Luftwaffe pilot, already nervous as hell, panics and tries to evade, and the entire rest of the Gruppe follows suit, for all the good it'll do them -- they're entirely too slow and ungainly to get a firing pass on a Typhoon that doesn't feel like letting them.
The bomber crews, on the other hand, have turret gunners who could get a "lucky" surprise hit in when they open fire.
At this point, the shit hits the fan.
WW2 anti-fighter turret guns aren't terribly accurate, and panicked shots are even less so, so while I'm willing to grant them a lucky hit on the first Typhoon, their wingman is likely going to recover from the surprise at the very least quickly enough to report they've just been fired upon.
"Active hostiles already within British airspace" is a worst-case scenario and the RAF reacts accordingly. Those things look like WW2 bombers, they fly in formation like WW2 bombers, and they just fired on British aircraft like WW2 bombers. We've tried communicating, it hasn't worked, time to shoot second and interrogate the survivors later.
You'll have to ask an actual military historian about just how much air defense - both on-land and on-sea - the British army had on standby pre-9/11, but even a modest amount by 2001 standards would be sufficient to turn at least the bombers - big, hot, noisy and very distinct targets - into shrapnel.
Their fighter cover isn't going to be of any use; every single thing that's in a position to shoot at them is capable of doing so from so far beyond a WW2 fighter's visual range that the first indicator of return fire would be when one of the bombers suddenly explodes.
EDIT A comment on another answer points out that at supersonic speeds the Typhoon doesn't need to ram; just the pressure wash from a close flyby will knock most WW2 planes out of the air with no hope of recovery. Of course, a WW2 bomber with a full and live payload of bombs crashing on land is a problem all of its own, but in all likelihood still better than letting it fly on and drop its payload over London...
Second edit Another important detail to note that may sound like trivia but winds up being lethally relevant: WW2-era anti-air fire, especially at night, involved lobbing big explosive shrapnel shells into the air and basically hope they'd explode close enough to a bomber to do any good.
The bombers didn't really have any kind of way to evade and needed to stay on their attack runs anyway so they were trained to just fly in a perfectly straight line and bet their lives on the fact that any single shot had extremely low odds of connecting; the anti-air defense bet the civilians' lives on throwing up enough flak that even 'extremely low odds' statistically became a good chance.
Modern anti-air defenses have radar and predictive tracking that have a good chance of picking off anti-ship missiles coming in for a kill. Their targets are big fat obvious blobs of heat and metal moving almost ridiculously slowly in a straight line. It's going to be almost impossible for them to miss.
