It is theoretically no more difficult to charge two batteries in series than just one.
NiMH chargers were all the rage in electronics magazines a decade or so ago. Modifying one to work at a higher voltage should be possible.
On the other hand it might be easier to just use 2 cheap chargers (presuming they charge correctly using the delta-V method) or provide two charging sockets and charge them one at a time.
Edit: I probably need to add that there are practical problems but they concern the batteries themselves. When charging multiple cells in series a weaker cell will often be both over charged and over discharged during a single cycle. Your 9V NiMH is already a battery, so you're stuck with this problem. If you make sure your 2 batteries are the same type and have the same initial state of charge (and cannot be discharged independently of each other) then you've done as much as I'd practically possible.
Oh, that brings up a question. Are the batteries in series to provide a single supply voltage, or do they supply a double ended (+/-9V) power supply? In the latter case there exists the potential for the batteries to be discharged unevenly which would be a big no-no for series charging.