Radiation and other such environmental factor certainly would affect the "shelf life" and effectiveness of all molecular compounds., so in this case packaging and storage would have to be controlled. Apart from these concerns the way molecules travel through the GI tract, the blood stream , the blood brain barrier and in fact all cells is most likely affected by gravity, so that micro gravity certainly would cause these factors to be different and likely produce unpredictable results. It should also be noted that drug metabolism and cell signaling pathways are also likely affected by microgravity and increased CO2 levels.
The simple answer is that we just don't know because the data set is very limited. The real solution would be to do more research in these environments because it is just as likely that while negative effects may be observed positive beneficial results are just as likely and may lead to a new and fundamentally different understanding of drug and cellular function.