The preferred time is usually June to September. I personally like mid June thru July. You may find that many of the trips during these time periods are chartered away and are harder to get....there's a good reason for that. June thru September also gives you the best chance of seeing whalesharks.
That is not to say that the diving suffers the rest of the year - in fact, recent trip reports from the Sea Hunter and Undersea Hunter have been raving about the diving. As was suggested before, take a look at the websites and scan thru their previous trip reports.
I've always dived Cocos with a Polartec and sometimes I throw on a 2mm hooded vest in case of a thermocline. A 3mm tends to be the standard wetsuit - but of course, if you hit a thermocline, you will be cold. That's potluck - in my past trips, the thermocline has remained below most of the time. I think that there is only one dive site (Ulloa or Lobster Rock) where it is almost always cold. The depth is about 110, and they do that dive mostly to look for the rosy-lipped batfish. Cold means lo 70's and maybe hi 60's. Otherwise, most dive sites are 78-80 F. BTW, not all dives have to be 100 ft. or deeper: except for the deep seamounts like Alcyone or Punta Maria, you can do 70-90 ft and still be at armslength distance from the hammerheads. Silverado, the cleaning station for Silvertips, is about 50 max.
Currents are unpredictable - sometimes they are mild, sometimes there is none, and sometimes it can get rip-your-mask-off nasty. There is very little swimming against the current - if that is what the concern is. Most of the time, you are either hunkered down on the rocks or drifting with the current.
If the concern is getting blown away, yes that can be a scary possibility, but if she strives to stay with the dive guide, that is less of a concern. Even then, that's where your trusted panga driver's eagle eyes come into play. Plus, I believe that all three boats issue EPIRBs to divers as an added safety measure - I know the two Hunter boats do, you may want to check on the Okeanos Aggressor. Don't forget, current is your friend - it's what brings the animals.