Ships can get First strike normally, I use it on my battleships and dreadnoughts a lot in your mod, are you going to remove that? Would that be a good idea? What about promoted wooden ships?
Second though: can some units be maintenance-free, or become maintenance free with certain techs? If they can, I have some ideas.
You can get DRILL for ships, which gets you some first strike ability... I'm not giving subs DRILL though, they're getting an inherent first strike ability (like Longbowmen or Skirmishers).
The ability to get DRILL (including for subs) has NOT changed... the only thing that has changed is that subs just get an inherent ability at first strikes (zero experience out of the dock and you get 1-2 first strikes). Adding DRILL promotions only adds to this ability.
Now destroyers will be immune to first strikes, and while it's main intent is to off-set the ability of Subs, it would (naturally) negate from bigger ships as well... but I don't see this as a problem for several reasons:
1) With experience a little harder to come by for naval units, and since subs and destroyers only show up in the Dreadnought Age and later, I'm assuming what experience folks are getting for capital ships is probably being assigned mostly to things like Gunnery Control, Damage Control and possibly movement bonuses...
2) You can explain-away the "first strike" thing in the fact that destroyers are small fast targets to hit, so are harder to just nail at long distance. True or not, it sounds good on paper!
3) If someone is fond of the DRILL promotions, it would only hinder engagements against destroyers... but if you're a capital ship, the way the Wolfshanze Mod is geared with bonuses and STRENGTH factors, you probably don't need first strike to sink a destroyer from a Dreadnought or Battleship... the DRILL first strikes would still be useful against other ship classes.
I put a lot of thought into this (as I do everytime I change some combat values or mechanics)... I think this is a plus-plus situation all around... I don't really see a downside and it's better then just trying to get subs to trump all units through other strength bonuses or something (or leaving them as-is which is still a bit weaker then I would like/think they should be)... they are still weak, but the first strike gives them some teeth.