I don't know what the disadvantages are to disabling hyperthreading. I have not noticed speed problems (although I have no comparison group). I'm a statistician and the only times, so far, that my cpu has switched to maximum speed is when testing some of the screensavers.
I know from the SuSE documentation that ACPI suspend functions do not work with hyperthreading enabled.
The computer not shutting off sounds like an ACPI issue. You should check on that subsystem.
As for being able to choose which desktop, that should be possible. On the login screen, there should be a menu button that lets you choose from a number of desktops, if gnome is not listed there by default it should be possible to add it (it appears in the list on mt slackware system). I don't know which file(s) to edit to add additional windowmanagers to kdm's list.