Yes, they can. It may not be the most desirable arrangement (compared with identical batteries), but it will work. Two six volt batteries in series are nothing more or less than a single twelve volt battery.
Connecting dissimilar batteries in parallel is less of a problem than connecting them in series, which should pretty much never be done. Different battery chemistries or significantly different technologies can be more problematic (e.g. having both AGM and flooded batteries with different charge requirements).