Ah, I see what you mean -- I hadn't thought about the tractor beams in this case. Something that is immune to tractor beams, like some sort of starship if you have unlocked it, could to the ticket, but that's probably a no-go. The EMP route is still potentially valid, though.
Ideally, earlier in the game when you see a crossroads planet with a planetary cloaker, that's a prime candidate for an earlier raid when there are fewer AI ships present. Once it gets to this point, given your ship mix, it's a matter of the EMP or the Nuke I think (those are the weapons of last resort, after all).
My point is simply to say that Planetary Cloakers can be dealt with easier earlier, often without missiles at all, especially if you tailor your tech unlocks toward doing them (transports, etc). But the longer they are left alone (but on alert), the more dangerous and difficult they become, until Nukes or simply going around (not an option in your case, obviously) become some of the last options remaining to you.
Depending on what you gained through your trench warfare, the strategy you use might still have been the best one for this game, and the Nuke is worthwhile trade for all that territory that you captured. I think your position looks pretty good, I'd be happy to have it in a game of mine, though the Nuke does make for some challenges with the AI's tech level, I understand.
