1stly don't over feed, thus reducing the need to vacume (I assume you don't over feed). Then any residual concerns over nitrates will be solved by the plants using them as food/ferteliser.
Also I think it would have to be a VERY polluted tank that affetced the barbles of a cory. I mean yes the barbles are sensative (they can also be worn down by sharp gravel), but they are there to find food and can handle a fair beating.
I have a well planted discus tank, and one bare bottomed, and the corries do well in both. I should point out that in both I do frequent water changes and DO syphon waste off the bottom (nearly) every day. I use a thin pice of tubing for this. Maybe take your gravel cleaner off its hose and use just the hose to syphon. Simply stirr the water as you "hover" the hose over any waste and don't touch the gravel....do this daily if necessary.
I hope this info can help you.
NOW let me tell you a story.....possibly the worst fish advice I've ever given!!
When I was a boy (yes one of those stories) I had a friend who's mother had a few goldfish with the biggest corries I'd ever seen in the tank. However I rarely saw them, because they lived in a 2-4" layer of sh*t. I mean she NEVER cleaned this tank (only ever topped it up), but everything was fine?!?! I was amazed by the size of the corries (and the goldfish and the fact anything survived) which periodically rose from this cloud of muck. Still I tell you (and will testify in court...LOL) that the barbles of the corries were fine, like I said earlier the tank would have to be VERY poluted before this was an issue. Still it will come back to the species, my friends mother had bronze corries and I would not try this with my scleromystax barbatus (corries?).
Which species do you have?
BTW Exellent that the plants are doing so well, sounds like a nice set-up you've got mate.