It is expensive work trying to outfit a ship. In my Flashpoint Campaign none of my players' NPC sailors has any armour. Most of them are common sailors. They didn't come equipped. One was a prisoner. They're level 4 so, in truth, if I counted their ship as part of their loot they probably would still be walking around with nothing but the odd Masterwork item. This wouldn't work out for them when the enemies they are facing are designed around certain equipment requirements (which really starts rearing its head around level 5).
At present, if they're lucky the NPCs they hire on might have their own equipment. There's certainly more of an urge to loot any daggers or cutlasses that haven't even been Masterworked. But they still have food, repairs, water barrels, crew payments, clothing, armour, and weapons to worry about in general.
So how do I handle it?
When I estimate how much loot they should have for their level, I don't count ship or NPC equipment. Its a rule of thumb, though, and I trust my players so I don't have to worry too much about them giving expensive weapons to NPCs to wield just so that they can then accumulate greater wealth. If they even tried it, I'd notice right away and tell them not to and they'd shrug with a smirk and say something like, "Worth a shot."
Now this isn't to say that they get so much loot that they can dole it out with impunity. They actually struggle a bit on the day-to-day level with reaching their wealth levels and are generally a fair bit below and that's fine. If they want to spend their loot on their ship than that's good. They'll be low for awhile but then they'll catch up.
This prevents them from over-spending on the ship because those short-term money constraints are an issue but it doesn't create a barrier of "Should I spend my money and grow progressively underpowered or should I not spend my money and have a mutinous crew and an ill-equipped ship?"