Seems ok to keep them on.
I have 2 500GB firewire 800 lacie drives raided together for a 1TB partition on a PMG5 for use with a uncompressed video in FCP.
The edit machines at my work tend to be used for more than 8 hours each work day, and even on weekends some times.
The backup system runs every night at about 10pm and since there is such a large amount to backup to tape, it take a while.
So we have started to just leave the systems on 24/7,
I occasionally turn them off if there is no work for them for a few days.
But one of the G5 edit machines has been in constant heavy use for about 3 or 4 months and has not been turned off once, maybe restarted once or twice, but the HDs have been on the whole time as-well.
I have not had any issues with the drives at all, and they are storing about 800gb all the time working with uncompressed SD video (So high bit rate video pushing the drives to there full limit)
Long story short, as far as myself and my enquires to other people running the same system and even lacie australia, they can handle being on for ages, and I never unmount them before restarting, the drives even turn them selves off when you shutdown.