Does using only 2 phases (400V) in a 3 phase transformer affect anything?
Does only using 2 of 3 wires affect the transformer or secondary
  circuit in any way?


Due to the nature of magnetization currents that flow, the centre common part of a 3-ph transformer core may have very little magnetic flux and hence can be made quite small without worries about core saturation. If you remove one of the three phase voltages, the flux in the centre-limb is no longer zero and has a value that is significantly higher than the individual fluxes. This could easily saturate that centre-limb and cause over-heating.



Picture taken from here. Other types/constructions of 3-ph transformers may not be affected.