whew that answer would be a book, not a post '-)
I own two composite boats (one is glass, the other kevlar/glass) and have owned two thermoforms (now just one, a SOT) have used them about equally over the last four years.
IMO it's not a case of which is "better". It is a case of which mfgr has higher QC.
I've seen fiberglass boats w. gel coat cracks and rear deck failures, or soft spots on hull or deck. Some of them, when taking a direct hit, expose voids where there is only gel and not much else.
I've seen thermoform boats that get brittle in cold water (40 degree range )or when stored direct on frozen ground. On impact some throw some long cracks, or lose a piece entirely (an irregularly shaped hole)
Either material will get torqued out of shape if tied down or racked improperly.
The integrity of the material depends on the mgfr's preferred layup, and their quality standards in using it.
Fiberglass is the timetested champion for light, strong boats (not just seakayaks, but other hulls).
It used to be a given that thermoforms would be lighter than fiberglass boats of comparable dimensions. But w. the advent fiberglass/kevlar and fiberglass/carbon, and w. the new vacuum bagging and even newer vacuum infusion in composite boats, that is no longer a rock solid conclusion.
Thermoforms (there are different patents of ABS plastics) have come on strong in the last 10 years or so, compared w. 40 years of glass boats. They are still a fraction of the market. Perhaps, in fairness, it is too soon for definitive judgments about which is "better."
Choose a boat based on the waters you want to paddle in, the kind of paddling you want to do, and fit/performance.