In Nex Pirates do not raid you if you are friendly with them, and, if they target your system, then your colonies do not seem to take a stability and accessibility hit. The pirate activity tooltip states that due to being friendly with pirates, their activity doesn't impact your colony.
I've literally never, and I mean never done bounties for the profit. Profiting off trade, then colonies, or, if you're so inclined, remnant farming more than covers most of my needs for spending. I kind of hate the bounty hunting system in this game. It always seems to send you to these relatively far-off places. Sure, I get that for exploration, since it seems that the further you go, the more likely you are to find all sorts of goodies, but the bounties never seemed worth the time investment for me, unless you need the rep or are enjoying it.
For the most part, I just can't be bothered always playing the whack-a-mole with pirates after I set up a colony. A lot of the time I'm inclined to keep doing exploring, trying to find good potential colonies to expand, getting blueprints etc. Besides, the annoying thing about pirates is that, generally, even if you destroy every single one of their planets, they still keep spawning.
Honestly, I tried the pirate friendly thing and it isn't that great. It's ok early on in the colony when you get less raids and pirates don't attack you on sight (although some events still cause them to attack you), but you still get the accessibility and stability debuffs from pirate activity, even if you are friendly which is the real drawback. It's not hard to build up enough defenses to stop the raids with no player intervention, but you have to destroy the bases yourself to deal with the pirate activity stuff, even in very late game. Also, not doing bounties really hurts income in mid game. You can't even do deserter bounties, they still count as pirates. I would maybe make an attempt to stay non-hostile very early on in the colonies life, but there's no point in doing more than that. Pirate base bounties are the freest money in the game right now.