While it is true that "the person's ability score and proficiency bonus are irrelevant" to crew firing shipboard weapons, that does not necessarily mean that it is the siege weapon itself that is making the attack. Neither the siege weapons section of the DMG, the vehicle-mounted weapons in BG:DiA, nor the shipboard weapons in AAG actually say who makes the attack roll: the weapon itself or the crew firing it.
If, as you say, it is the weapon itself that makes the attack roll, then yes, that does dramatically limit what can influence this roll. The D&D combat system is built around creatures attacking creatures, and there are any number of ways to influence these attack rolls. When, as you say, an object attacks an object, rules support for influencing the attack roll is rather slim indeed.
However, there are a few things that can affect such a roll:
Take Aim
The 'Take Aim' Special Action afforded to ship's officers in GoSM (198):
Special Officer Actions During an encounter, the captain, the first mate, and bosun each have access to two special action options: Take Aim and Full Speed Ahead...
Take Aim As an action, the captain, first mate, or bosun direct the crew's firing, aiding in aiming one of the ship's weapons. Select one of the ship's weapons that is within 10 feet of the officer. It gains advantage on the next attack roll it makes before the end of the ship's next turn.
It is interesting that the GoSM rules are the only set to specifically say that it is the siege weapons themselves that make the attacks (rather than the crew) and also the only set to specifically give members of the crew a way to influence these rolls.
While your question was prompted by Spelljammer, and there is no way within that ruleset to improve the weapons' rolls, the Special Action referred to in the GoSM rules are by no means a far stretch. There is little difference in theme or mechanics between the captain of spelljammer and that of a sea-going vessel, and you (or your DM, if you are a player) could easily make such a special action available to a spelljammer captain. Indeed, I don't see why a naval captain could not become captain of a spelljamming vessel (taking their special action with them), since there are no rules requirements for either position.
Bountiful Luck
Xanathar's Guide to Everything includes a racial feat for Halflings called Bountiful Luck (pp. 73, 74):
When an ally you can see within 30 feet of you rolls a 1 on the d20 for an attack roll, an ability check, or a saving throw, you can use your reaction to let the ally reroll the die. The ally must use the new roll.
Note that as written, a halfling with this Feat can use it on any "ally", not only an 'allied creature'. Since there is no game definition for what constitutes an ally, a DM might consider the siege weapon itself to be working toward a common goal with the halfling, and thus allow the halfling to grant a reroll on the attack roll, thereby making the siege weapon's attack more accurate.