I think that, if a new role is included, it should fill a niche that hasn't been filled yet- no overlaps. The Saboteur role does alright in that category.
The pilot controls the ship,
the gunner damages and disables the enemy ship, and
the engineer keeps the ship from being damaged and disabled.
The gunner and the engineer both have roles that are intertwined, but the pilot only has other pilots to worry about. Maneuvers are what the role is all about: ramming, lining up shots, evading, hiding, and losing distance.
A counter to the pilot's role would be something that is aimed at removing the effectiveness of those maneuvers, may it be through disabling, finding/spotting, and in general, making the pilot's job harder. However, all of these counters are filled by the current roles. Finding and spotting is filled by both the engineer and gunner if they choose the spyglass, the gunner acts as the disabler by attacking certain guns, and enemy pilots are the primary difficult objective due to their control of the entire vessel.
I have not read many responses to this post, so I am simply just stating my direct response to your idea.
The monkey wrench (which is another word for pipe wrench, which does exist currently) would act like a manual flame charge dispenser, that also nerfs systems. Unless this is a permanent thing for a minute or something, a few whacks will remove the hindrance, which would be a complete bummer due to the fact that the saboteur would have had to board the ship in some timely fashion, and a debuff that could be removed with a quick repair would not be a good payoff. The constant, irreparable damage would be unfair if a sabo was able to hit the hull, engines, and balloon, as it would require constant attention from an engineer.
The blackjack could be a completely overpowered tool if it wasn't balanced correctly. The way you put it, it seems like once a saboteur is on your ship, you need a blackjack to get him off- what happens if there isn't a sabo? A constant pest would ruin a ship's chances. This would make having a sabo a required thing in order to counter itself. If an entire team went sabo, and launched itself onto a ship pirate style, they could stunlock the crew with blackjacks while they nerf their systems with damage over time, and then allowing an ally to destroy them as the unpiloted ship flys away to safety. Once the ship dies, they can all just respawn on their ship half a mile away.
Deck buffer is clever, but, once again, going through all of the hoops required to get onto an enemy ship wouldn't really be worth just mildly inconveniencing people by sliding around. If anything, they could just slide into walls in order to stop momentum and keep on repairing. And those that stand still, like the gunners and pilot, would not really be affected. Your own ship would be better off with an extra gunner, than impeding enemy engineers from moving, not repairing.
Bull horn is a captain slot, which means that all sabos would take this. The trolling and ear-blaring, speaker-bursting spams would be terrible. Assuming that a ship has to be close to each other in order to board(You even said, "No need to add extra boarding mechanics"), the act of shouting out positions doesn't sound very effective- unless the sabo plans on being on the ship for a very long time, or even after his own ship is destroyed. This brings me back to the fact that a sabo would need to be around in order to counter a sabo.
And lastly, "Box with two eye holes cut out of it™" is a counter for enemy sabos when you are on an enemy ship. This makes it a fight to see who can get a sabo on the other ship first. Once that happens, he can just sit there and effectively remove a player from the game, because he has to be on the lookout for that camping sabo, or else his ship will be tormented. Sabos counter sabos counter sabos. Its starting to sound like this role is just going to be fighting itself, with little help to the overall fight on both ships. Because the monkey wrench is a default loadout choice, it also means that their main intention is to board. However, they have to be on their own ship to fight other sabos, which renders every tool, except the blackjack, completely worthless. I don't think that's a very good choice.
Stuffing Lochnagar Shot into an enemy gun would be an annoying, ship-breaking choice, so why even bother using the monkey wrench when you can disable the ship's ability to fight?
The Saboteur role is an interesting idea, but I feel that roles would have to be centered around your own ship's operations in order to keep it fair. Coldcurse mentioned listening to enemy voice chat, having a radar, and seeing health. All of these are supportive, and would not ruin a ship's chances if it didn't have those tools. However, sabo would become required in order to deal with itself.