Greetings!
I think that (but I am not certain if) the disable filesystem check flag through hijack only applies when the filesystem mount counter exceeds the threshold (30?). Now, if there was any damage or other error on the filesystem (from leaving the drive mounted read/write and restarting the player, for example), I believe that emplode will still perform that check in that case.
Note: on an 80GB drive with older players or players with applications running in the background (less RAM), there is a chance that this fsck that emplode kicks off will fail silently. (Usually, the error you will not see is that fsck cannot allocate enough memory for the table space for Pass 5 of the fsck...) You will be able to do your sync, everything will look normal, but the next time you sync you will again have a full filesystem check because the "dirty" flag was not cleared. This situation can only be cleared by fsck-ing the drives
manually.