In my universe 500 to 700 years the navy is deployed to eliminate the cult stronghold on the planet of OgallyBoogally. The bunker is a kilometer below the surface and covered by lots of armor and point defense. The navy didn’t bring any marines so just landing ships and storming the bunker. I thought it would be cool to have a bombardment vessel armed with lots of missiles and a big railgun. The missiles are similar to the robust nuclear earth penetrator and are nuclear. Does this ship make any sense?
So it's not that your design of "lots of high-penetration missiles and a big railgun" is bad. That seems plenty enough to ruin a ground-based defenses day, even if it's underground. (You don't even need nuclear-tipped missiles, a sufficiently fast-moving titanium rod will get the job done sans fallout) It's that there's no need for it "just" to be bombardment vessel. Such a ship seems loaded out in a fairly standard "scifi-warship" sort of way. Is there a reason for it NOT to be your ship-of-the-wall? There are no laser weapons that would suffer from the planet's atmosphere. It's a stationary target a ship designed to hit other ships would easily be able to nail. The only thing you might need to do to change it's armament from ship-to-ship to ship-to-planet weaponry is replace the nose cone/warhead of your missiles so they don't burn up in atmo. But that's trivially easy for a warship to carry. (I bring 20 missile engines, 20 anti-ship warheads (or maybe more, if you want special anti-escort/anti-fighter/anti-capital ship versions) and 5 anti-ground warheads "just in case" or whatever mix makes strategic sense. Stick whatever warhead you need on your missile pre-engagement and you're set!
If you want a "true" bombardment ship (ie: something that's superior against planetary targets but not super useful against enemy ships) I'd suggest a specialist light-cruiser type vessel. Build it around the obligatory Real Big Railgun. The tungsten Rods from God will be its primary anti-ground device. hard to spot, hard to track, hard to knock out en-route. Targeting a facility once spotted is trivial because it can't dodge, but FINDING said facility an AU out might be hard. Ship sensors, after all, are usually meant for finding other ships against the blackness of space, not one base/installation on a planet that has other sources of heat/light/radio traffic. So your ship's other space can be given over to an impressive array of sensors, detectors, active and passive scanners, and intelligence/targeting officers to identify critical infrastructure. This superior sensor package (because governments are cheap) is angled in a single direction because hey, EVERYONE knows where a planet is! No need for 360 degree coverage. Plus sensors that can tell an underground command bunker from a coal mine might not be great at IDing ships anyway. It's on a light cruiser chassis because it doesn't have to be well-armored (it's beyond the ground target's ability to actively fight back) but it could probably do with being fast enough to get in/out before an enemy patrol finds it.
Meanwhile, in a ship-to-ship or fleet action this thing.... isn't great. A single main gun that can easily miss a maneuvering target, an overly-specific sensor array that may or may not be the match for "normal" ship sensors, and a frame that isn't meant to be charging into the fray. But it's cheap (light cruisers being much cheaper than a battleship), does its job REALLY well, and in situations where you still need "boots on the ground" would probably be a fantastic invasion Command and Control ship. Your Navy wouldn't want to make a ton of them, but a few certainly would be a benefit!
TL/DR: Your ship is just as good a warship as a bespoke bombardment ship, so either keep it as an all-in-one, modify the design, or be prepared to explain why a seemingly-reasonable design isn't any good ship-to-ship.