Ruth,
I am assuming the big sponges were pretty dirty when you cleaned them. If so, they were doing the job they were meant to do - which is mechanically trapping detritus. By removing the sponges, that detritus is now staying in your system, unless your other means of detritus removal will do as good a job of trapping and removing the detritus.
IME, weekly cleaning of ALL mechanical filters is a must, especially if there is a nitrate problem. Larger, more frequent water changes are also necessary with high nitrate. I would even go so far as to do two 30-40% water changes in a week for 2-3 weeks to get nitrate as close to 0 ppm as possible.
At any rate, monitor nitrate over the next month or so to see if removing the big sponges actually did anything for nitrate levels.
HTH
