The next version of MultiHack will have this feature. However now it still possible, with just a bit more work.
When you install a hack, select "Overwrite Source Files", then install. Keep doing that for all of the hacks you want.
Then upload any changed source files, just look at the file dates.
It isn't a clean method, but... works.
If I ever get into the mode again for coding on MultiHack, there are many features I want to add, but with the basic lack of hack author support I am unsure if I am going to continue. Many people at the vB forums have asked me to code something for them, and have setup test boards specifically for me to play around... we will see.