I'll bet you could generally run almost all of these engines for ONE sortie at max power indefinitely, until the WEP or nitrous tank ran dry, and NOT significantly "damage" the engine to where it would degrade performance.
(There may have been some engines that couldn't handle "overboost" or "overrev" or whatever, but I haven't seen any accounts of this).
What probably WOULD happen is that the engine would be "thrashed" or "wear out" sooner, i.e. it might fail on a LATER sortie thanks to the abuse YOU gave it earlier. But that failure might happen at cruise power, not when you went to WEP.
IMO the penalty for disregarding the flight manual engine restrictions was decreased engine life, not imminent failure. How do you model that? Can't do it without opening the "random engine failure" can of worms.
Say you normally have a 5% chance of an engine malfunction (as opposed to 0% now). For any given sortie, you have, say, 10 minutes of WEP, and 10 minutes of military power available (different for each plane). Every minute you spend at mil/WEP beyond that goes into your "engine life factor" for the NEXT sortie and modifies the 5% malfunction probability upward. Fly around in mil/WEP for 5 straight sorties, maybe you have a 50% chance of an engine failure on the next one.
Probably pretty complex to program tho...
As for full engine management of prop and mixture controls, what purpose would it serve within the context of the sim? In RL, you're really talking about the difference between "optimum range" and "optimum power" when you start tweaking the RPM and mixture settings. In the sim, you're pretty much always looking just for optimum power (which is EASY to set up in a real plane) and you don't have much need for optimum range because of the arena size and availability of drop tanks. So sure, it's nice from a "realism" standpoint, but is it going to change the way you play the game enough to justify programming it? I suspect almost everyone will just program a joystick button to "cruise" and another one to "fight" and that'll be all the "tweaking" they need to get the most out of "real" engine controls.
I suppose with a big enough arena, and carefully modified fuel burn settings, you could "force" folks to learn how to use the engine controls properly. Seems more suited to scenario use tho...
--jedi