In fact, the FCC's response to the bot activity was to point out that they aren't permitted to delete the comments, though a former FCC special counsel was quoted as suggesting that the FCC "might have an obligation under the Administrative Procedure Act to remove fake comments from its consideration."[1] But "removing fake comments from its consideration" isn't the same as actually deleting them, so I'd imagine that just means labeling them as "likely fake" and ignoring them in their deliberations. The same would apply to official FCC complaints. The FCC might ignore them, but they can't outright delete them without violating the law.
0. https://www.law.cornell.edu/uscode/text/5/553
1. https://www.wired.com/story/fccs-broken-comments-system-coul...
The complaints likely won't go anywhere anytime soon. But when Pai's successor is working to repair the damage, there's a decent chance that one of the things they'll have to do is go through the agency's records to figure out what was ignored. Having a record of the complaint will at least give them options in the future.
So file the complaint, even if it's unlikely to matter in the short-term. :)