When is a 6.3V capacitor not a 6.3V capacitor?
6.3V rating is okay for 5V, provided you meet all the other datasheet limitations. 

The ESR appears to conform to the Murata datasheet (> 15m\$\Omega\$), so you should be able to put one of those 1000uF capacitors on each converter (unless you start worrying about the tolerances, but it's probably okay). 

The ripple current rating of 755mA (if I read the data correctly) could be an issue causing the capacitor to overheat and fail, but it's difficult to predict what that RMS current will actually be. You might want to either measure the current under worst-case conditions or check for any measurable heating of the cap under worst-case conditions. Worst case is probably maximum current load.