I tend to try and do top down. Prince rqts naturally do this, plus its easier doing them 2 piece as they usually have double grommets & hard weaves.
I also see a lot of rqts where the manufacturer has strung it bottom up.
To be honest tensions are lower and I sees squash rqts as structually sound as a tennis rqt, so bottom up should cause any problems. As for head shapes, I see no difference afterwards.
Head IG Prestige MP; USRSA MRT, Wimbledon stringing team since '04; Babolat stringing team '10-'13. Twitter - @therqtstringer