Vitunguu means onions. Saumu means 'a fast' like a period where you don't eat something. So I'm guessing the root meaning of this is onions that are on a fast?
I've never heard garlic being referred to this way, as far as I know garlic is thomu or thom.
I never heard thom or thomu for garlic - maybe regional variation?? (if not; could it be possible you are confusing it with another, possibly similar, language?)
My guess is that the "th" in the Arabic "thomu" (ثٙوم) became an "s" like it has in many borrowings and offshoots. So perhaps in Swahili they say "garlic onion" instead of just "garlic" which would make sense if it's not common in East Africa.
In Luganda(A language in Uganda);
Garlic is called "Katungulu simu/chumu";
Garlics = "Obutunguulu simu"
An Onion="Akatunguulu", Onions="Obutunguulu"
I am fairly sure it is your first alternative. Compare "miguu" (legs). When there are double vowels, both should be pronounced.
Yes, vowels should always be pronounced separately, and the stress is on the second-to-last syllable; there can be funny minimal pairs - so if you do not pronounce one, it may take on another meaning. (see "kufaa" to be useful/fitting vs. "kufa" to die)