Generally speaking, any aas - not just the hard stuff, but the presence of any aas within the time of 1 menstrual cycle will most likely shut off the flow but it does NOT completely remove all the accompanying symptoms -- mood swing, bloat, cramps, etc.
Other stuff mentioned can cause ammenorhea as well -
- low bodyfat - generally below 12% but is very individual
- major change in physical activity or diet, even stress
If AAS is involved, barring the above issues, normal menstrual flow should come back once the AAS has cleared your system and a new monthly cycle starts (ref: detection times to get an idea of when stuff should be clearing your system - var & winny should clear within 3 weeks, so you could expect a normal cycle to start up again within the next month. Harder stuff can be longer.)
ACK -- re: your wife's depression, etc. Take a look at the degree & speed of increase of her training - max weights, volume during the duration of her var cycle. If there were significant increases in a short period of time you can absolutely expect that the weak links in her body, e.g. joints took a beating not having a chance to build up & accommodate the increasing weights. AAS also tends to mask those pains that normally take longer to heal. The depression, hairloss etc. that sounds more like either a hormone imbalance or a thyroid issue. Since the var should be clear after 3 weeks you might want to get her in for a standard physical and get all her hormone levels, thyroid, etc. tested. Just so coming down from the higher T levels may not be completely done yet, you might want to let it settle for a while longer - see if the issues continue for say another month and then go in to see an endocrinologist or just get a standard physical to eliminate any obvious causes. Or things may just pass after a little bit more time.