The first thing that needs to be determined is if the "clicks" are on the original mixes. If not the engineer may not have had proper clock. If this is the case it should be redone properly.
If the clicks and hiss were there before and the mastering eq brings it out more the engineer should have the proper software to fix them(unless there very bad).

Proper "pre mastering" should be the last step in the audio processing. Anything done after opens a pandoras box of things that can degrade the signal like clock issues, jitter, dither...
All reasons to work with someone who understands all this so you come back with a master that sounds at least as good if not noticably better than the mixes.

your going to have to decide that. It most likely will need work after your clean it up. Probably better off starting from scratch. As my grandpa used to say, "pay a little twice".

Thanks so much for the quick responses guys.

Apparently, most of the stuff "appeared" after the mastering. i wish i wish he had taken my advice and shelled out a little extra for a more professional mastering job. He apparently doesn't have much left over for any remastering. On the bright side, it's a rather rough-edged electronic album, so a lot of the noise is masked behind the music, which at times is intentional noise... So it could be worse. Thanks again.

The noise was most likely there to begin with, he just brought it up. When you do any kind of noise reduction during mastering, the ME compensates for this and eq's accordingly. In this case, when you take out the noise, the track may appear to be too dark because the ME was eq'ing with the noise in and may not have pushed the high end to where it should be. So now when you take all this High freq information out, your going to have a lack of high end in the track. Keep that in mind.

Thanks Michael. I will definitely keep that in mind. Do you think the best bet may be to just have the noise reduction kick in when the dbs drop to a relatively low level (i.e. fade outs and ins)? (does that make sense, or do i have it completely wrong?). Also, it looks and sounds like the clicks seem to mostly come right before several ms of silence (where a reverse effect was used), so they're relatively easy to fix. I'm supposed to get a listen tomorrow night of the unmastered version - I am curious to hear the difference. Thanks again for the feedback.

Really depends on the kind of noise and if your able to get a good finger print of it. But i've done just the in's and out's manytimes if I can't get it to work well within the song.