nothing wrong about removing weapons. You win through destruction from inside, not outside. Largest ships will need up to 5 boardings. You can help with assassins - they got talents that execute random officer(cpt being one). Like
LordofSyn said, board win cards are STRONG. Single boarding gives 100+ xp to crew that executed it.
That being said, once you get that raptor ship(bad name imo, it looks more like raider from battlestar galactica, not raptor) you will have enough space. All you really need is 1 torpedo to cripple enemy ship in round one to prevent escaping... And you probably dont want it on scout.
Only issue with raptor is that it still got same crew count as scout(with extra officer). It is doable though to have all skill checks at 200%. Im still in process of optimizing head count for perfect spy. Will share once im closer to being done
. Spy style cpt synergy with specialist crew is amazing for all: flying around, spying, boarding.
1 solid armor mod on ship will set you up.
for example cards like 'Raining Steel'. Ive tested with 3 crew members having 3-5 of those and only single one gets fired on single crew member. It also works for cards that are fired against your enemy, like 'First Blood'. Due to that my splash to assassin feel bad now.