What is the effect of load on 15kVA 3-ph in,3-ph out UPS and 15kVA 3-ph in,1-ph out UPS?Does 3-ph in,3-ph carries greater load than 3-ph,1-ph out?

This will depend on the specification of the UPS. You pay your money, you take your pick. I assume, given that you are looking at either output option that you are purely running single-phase devices. In which case you will need to carefully balance your load on each phase, also considering when you will be drawing current on each phase. It's no use balancing the loads on paper then finding that all of the devices on one phase are permanently running and the otheres are only rarely running.

Ideally running the UPS at full load (allowing for PF) will give you greatest efficiency but the other factors to consider are peak loads such as inrush currents.

Another thing you may wish to consider is cable sizing, a single phase output will require a substantially thicker cable to carry the larger current.