My cannister filter has plastic rings and ceramic chips for bio-filtration (bacteria lives and grows on this) and a basket with foam pads and fine filter wool at the top. I only open the cannister every three or four months (as it is huge and doesn't need it) and I rinse everything in tank water except for the floss - which I run for 10-15 minutes under the tap to get it clean. Every 6 months I will change the floss completely for new stuff. I also use a pre-filter sponge over the intake and rinse this under the tap every week - this catches most of the debris before it enters the filter.

Yes, bacteria may well grow on/in the sponges but my filtration is large enough (with the ceramics and plastics) that I can rinse the debris-catching parts under the tap with no ill effects on the nitrogen cycle in the filter.