The Viper 95 runs hotter than a viper 200 because it is a single supply drive. The incoming main voltage is regulated down to power the drive logic and the encoder, so there can be a lot of heat dissipation.
How many mA does your encoders draw ?
If you mount them well on the edge to an aluminum chassis or plate thats all you should need for a 50 volt input. When they are run above 60 volts, heatsinking would be necessary. BTW, thats why encoder current on the Gecko320's is limited to 50mA because it works the same way.
I'm using 2 voltage regulator's though, one for the drive logic and one for the encoder, so you should be able to run up to 80mA encoder current. But the power supply voltage plays a part. The higher the PS voltage, the lower max encoder current available. At 90 volts, i wouldn't recommend over 60mA encoders.