If your not using the community (CSSU) version this was much improved regarding performance and bugfixes. apt-worker being 40% faster than original code.

The way I understand it there will always be a limitation on how fast HAM can be due to maemo packages having there icon data encoded in the control files.
Minimise the amount of repos you have enabled will speed it up, if you don't wish to edit the update timer value hidden in the backend.