The capcaity in terms of stored energy is the same in both cases. Step-down converters generally tend to be more efficient than step-up ones but for properly optimized designs the difference is not very big. Also your 12V and 24V betteries all contatin multiple cells so if you are going to use 2 similar batteries then there is mot much difference in terms of ballancing or expected wear as well. Also 12V lead-acid batteries can only safely be discharged to around 8V and it is well above what any proper DC-DC convertter can go down to so there is no difference as well.
To be honest I would probably go with a series connection because of slightly less active losses (higher voltage -> less current) and slightly more efficient and more readily available convertors but there is not much to it, you can go with whatever you like or depending on whatever equipment you already have available.