Taking out tubes like this will tend to raise power supply voltages. Part of the change you're hearing maybe related to the higher B+ to V1.
Whatever, I can't think how any harm may be done (they're 450V B+ caps in the V32).
Regards V3, see if removing it improves the sound any, if so then take it out.
Keep the tubes safe, not rolling around in the bottom of the amp, as they may be needed as spares in future.