Yes, it should work well. Maybe do a test before -- don't remember exactly how IQ deals with mht external files if you you transfer the file and sndb folder to your card, but it shouldn't be a problem if you DON'T move them apart (the path should be relative).

In most cases, you probably don't need the SNDB folder (containing mht files) anyways, especially if the option to keep MHT content in the database is checked (Options-->This file-->Data Storage --> Save a copy of the MHT file...)

Make sure you're running the portable version by "Help>About", as there is a portable and a non-portable version.