It should be done like in terraria, you have chance to drop unique staff or sword from any boss. It's hard to play with dual wielding swords right now. Also mobs should have like 0.1% to drop something unique.
NOPE NOPE NOPE NOPE SO MUCH NOPE. Now seriously, SB shouldn't add Terraria-like boss (Or drops, period) drops. Quite a few SB players already played Terraria, and the random drops aren't liked in that game, since they tend to turn into a massive amount of grinding that gets really tiresome and obtaining said dropped items becomes a chore.
So what u want to do after end of quests? I'm sure more people wants something that and like it was before in starbound (summoning maybe mini bosses).
That was even worse. You shouldn't assume people would like to have to kill the same boss ten times to get the best weapon of whatever kind they prefer. In fact, I'd say that, if that were added, the Discussion thread would be quickly flooded with complaints. A better option would be a post-Ruin questline, and more interesting Colony mechanics.
They already designed unique drops for each boss: Erchius Horror... Erchius Eye Bone Dragon... Dragon Head Big Ape... Miniknog Launcher Nox... Solus Katana Etc... Not all of them are implemented yet I think. But the weapons are functional, so they just have to update the drop pools. None of them are that overpowered compared to what you probably went into the fight with so I don't think there's much point to get them aside from a collector's view.