Holes won't much affect radiation, which is significant for a power valve like a rectifier. They will reduce the glass temperature a little, which will reduce heat radiation from the glass itself but do nothing about the heat coming straight from the anode through the glass.
I would leave a couple of inches gap as a minimum.
I'll second all of that - for me 2" is the minimum for GT style envelopes, for bigger G types I generally allow even more. The components inside doing all of that radiating are generally in a well defined plane and do a better job of heating things nearby than you would think from the shape of the envelope.