In the case you describe there is little practical difference. But I would lean toward two 24V batteries in parallel. They are easier to keep balanced, and as stated earlier, if one fails you still have a working system. Just make sure you connect the positive and negative load wires to opposite batteries. Do not put both on one battery.
With two 12V in series (assuming the batteries even support being in series) it is really important that both are at the exact same SOC before connecting in series and you might need to redo that once a year or so if the SOC starts to diverge over time. And if one fails your whole system is down.
But neither setup is really any better with regards to performance. You can lower life expectancy in either case if things are not setup correctly. Two 24V in parallel is a big win for reliability from the point of view of the whole system if one battery fails since you can keep running on the remaining battery (at a diminished capacity of course).
Full disclosure - I have two SOK 12V 206Ah batteries in series because they didn't have 24V batteries at the time. Once I got the two to the same SOC they have been working just fine. If they had the 24V batteries at the time I would have bought those instead.