Will the uninstalling of apps leave file cruft in the root (Android's subsystem)?
Not in the internal filesystem, but it may leave files on the SD card.

Apps on Android are only able to write on two places within the filesystem


/data/data/&lt;packagename&gt;
/mnt/sdcard/ or /sdcard


The /data/data/&lt;packagename&gt; directory gets deleted when you delete the app, so the only place where file cruft can be found is the SD card.