IIRC, despite the fact that the various weapons aboard a Spelljammer takes multiple actions to man/load/fire, ships (at least according to Ghosts of Saltmarsh/Aqisitions Incorporated) can take up to three actions as long as their number of crew members don't dip down a certain threshold. As for attacking the Captain or what not, it's quite possible but there is also the possibility that depending on the area WHERE the opposing Captain is at, there could be 5E cover rules in play. Ducking behind a mast/guard rail/or whatever would offer some degree of protection. Whether or not it overcomes the Damage Threshold in the process is another thing altogether.
As for attacking things, there is not only the Siege Weapons aboard a Spelljammer vessel, but also other things, such as Archers and Spellcasters, that can be used to target opposing crew members and/or Siege Weaponry.
I think as well, there is a rule, in Saltmarsh, where the level of a spell you cast gave you a number of D6s you would roll. And the number you rolled on the d6 would've been the number of opposing crew members incapacitated/downed or what not. Perhaps a similar approach could be used for Siege Weaponry when it is used to attack crew directly. (of course, that's for opposing crew that uses the Commoner statblock i would assume. Any special character/npc/whatever would get saving rolls.)