Yeah. It's not a modern compounding form as with -(s)U(n), it's an older blend of adjective+noun that underwent some phonetic changes.
kap = cover, plate, container, vessel
So kaplı = something having a covering, or plated (~shelled)
bağa = a very old Turkic word for frog/froglike animal, never used on its own in Turkish
So kaplı + bağı, the ı rounds because of the b in front of it and an m appears just as a buffer sound -->kaplumbağa "shelled froglike thing" :D
Similarly tosbağa comes from tıs or tos, depending on who you ask, an onomatopoeia sound for hissing. So tosbağa is a "hissing froglike thing."
It's the same in German and Danish (and, I presume, Swedish and Norwegian). In German it's Schildkröte and in Danish, Skildpadde. Schild = Skjold = shield, and Kröte = padde = toad.
about tosğaba my mother doesn't agree with your theory. She relates "tos" in tosbağa to toz meaning dust. because these reptile species are land-dwelling and dust is one of the features of where they live.
Actually, it was originally a glottal stop in Ottoman Turkish and still is in some eastern dialects! However, sound change over time has eliminated the glottal stop in standard Turkish.
No glottal stop.
Between two like vowels it just lengthens the duration of the vowel noticeably. Because of the fast pace of spoken speech such length distinctions get dropped, many Turks often learn words with a ğ between two like vowels incorrectly. (There are about 50000 results on Google for kaplumba!)
Between two unlike vowels it acts like a glide to help you move from one vowel to the next (and will sound a bit like y or w).
(Take note, though, it varies by dialect!)