It would be much easier to remove the males if the plants were separated. It's not impossible however. You would probably end up with some dead roots in the medium and water, but until the end of the grow that probably wouldn't hurt. Roots will get tangled up, but you can separate them as best you can, and the ones you can't get, you can cut off with scissors. This is not optimal of course. It could, temporarily at least, slow down growth of the ones who's roots you cut. Overall the system could work and you would end up with weed.

It's really best if you are starting from seeds, to sex the plants before putting them in a system. Knowing that you are starting with females solves so many problems.