Fixing the typhoons 'annoyingness' to use is independent of whether it is OP or not. They're separate issues.
We can buff the sub, but vs typhoon only damage and speed would help. Damage means it starts 3-shotting itself, which means that sub vs sub battles become much less dynamic (they're already not as good as they could be). If you increase the subs HP too, it becomes stronger vs Hunter as well as vs Vette.
You can nerf the vette, but this hurts it vs Hovers. Particularly its speed and HP would help vs subs. Losing either speed or HP would make mace-kiting much worse, which means it might need to get more range as well (changing its weapon in any way doesn't effect it at all vs subs, so its a good swap to make to increase the counter dynamics while keeping its power unchanged). More range means it's better and probably destroys the whole mace kiting dynamic- Scalpel has more range than mace (440 to 350, vette is 270) and similiar speed (2.1 to 2.2) but is it good enough to replace Mace for kiting? More range for vette also lets it fire further inland (not a huge issue).
You can see how complex this gets and this is exactly what Google and I have been discussing regarding this matter, only we've also been factoring in the balance of the new amph units and how these change will effect them (esp, how Amph power must be pegged to Sub power, otherwise, as a submerged unit, it is just a more effective land-walking sub).
Slowbeam ship would not fix vette running vs subs. If it is a ship the vettes will eat it alive, how is it going to keep ships in place long enough for subs to kill it? So you're using slowbeams + vettes vs vettes? Bad dynamic. The Sub would need slow or EMP on it's Torpedo (Actually I'm liking this idea the more I think about it).
I wouldn't be against a slowbeam unit for -hovers-, since they need more units, and we only have 2 units that use slow. This would allow you to actually use scalpels effectively (I think the major reason we see so few Scalpels when compared to Janus is the lack of synergies and the fact ships are so fast).