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Your suppositions are correct about what will happen whenever you hard reset or flash a new CE ROM.
The "hard" way to get around this is to create a custom settings OEM for yourself to include in the ROMs you build. You would then include the reg settings for the programs you installed to the extrom inside your custom OEM, as well as shortcuts to get copied to \Programs for those apps. End result is that whenever you hard reset the reg entries go back in and the shortcuts are re-created. I've been doing this for a while with TomTom, Slingplayer and a couple of other apps with great results.
The "easy" way, as you've said would be to just reinstall the cab files every time you have to hard reset or change ROMs. If you don't have the skills yet to create OEM packages then this is the right way to go, since you'll be sure that the everything gets inserted properly and in the right places. You still benefit from having the extra storage space--it just requres a little more work on your part each time you hard reset.
Oh, and keep in mind (if it wasn't obvious) that you have to unlock your extrom after every hard reset and ROM flash. The bootloader automatically relocks it during a hard reset.
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