what do you want to do with iTunes?
if you mean using tunes from your iTunes library, then FCP and ST wont play well with the MP3 or AAC formats.
they like AIFF, WAV, and SDII files (i might be out of date with the SDII)
it;s not an application incompatability, its a format incompatability.
and iTunes can be used to convert the format, so it;s can be seen as quite a usefull app in conjunction with the other two,
although it;s not the only app to do the conversions.
compressor will also work.
nick