So this is a surprisingly hard problem. These engines are quite simple and there's few vectors for sabotage or attack directly against the core engines. There's no electrics for EMP or ray attack, (there's no spark plugs). They're hard to throw out of balance with resonance or vibrationexternal vibrations or electromagneticmagnetic fields due to them installed on padding to minimise acoustics. They run with gas contamination down to as little as 5% oxygen. An attack on the fuel supply or oil will work, but that's old news and you want emerging.
The only real attack vectors I can see are those things which are technically external to the engine but control its integration with the rest of the submarine. The clutch control. The snorkel vent solenoid. The throttle. The alternator. The temperature, vibration, and pressure sensors. And the network box that allows all that data to be monitored and controlled from the bridge.
If something that was test deployed in 2010 can be considered "emerging", I'd suggest a StuxNet virus variant targeting some of those systems. (This was a virus that spread across the internet until it found it's target, and then blew up the targeted uranium centrifuges by messing up the careful spin rate, and reporting different state to what they were actually doing).
For example, the virus tweaks the fuel / air ratio per cylinder such that the power generated on one side of the cycle is significantly stronger than the other, stressing crankshaft and piston and related components and increasing wear and tear on difficult to replace parts. The virus also tweaks the reports from the engines accelerometer, reporting that vibration is within design limits (and the acoustic dampening engine mounts make it hard to notice the problem by hearing the difference).
The virus doesn't need to even be delivered to the submarine. Attack a weaker link - say the receptionists machine at the office of a contractor, the virus spreads onto a usb key from there onto a meeting room pc used for presentations, where someone running a training session and needs to screen-share plugs in the handheld computer used to service the embedded systems on submarines, infecting it. That then uploads the virus the next time it's used in a service.