Callum: the slowness of modular DocBook XSLT stylesheets is in the chunking code, as I found out a while ago. You will find that if you turn off chunking (ie. produce one huge output file rather than many smaller files), the processing time will be cut in half. Interestingly, the older DSSSL stylesheets showed the opposite behaviour.
One thing that might be interesting would be to try porting gtk-doc over to using Shaun McCance’s new XSLT stylesheets (there are more details on his website). If these are suitable, they could give a significant boost to building API and user docs.