I think for it to really become a problem it usually requires a combination of both (excess thiaminases and insufficient thiamine). I think the biggest problem for predatory fish happens when exclusively eating feeders that contain a lot of thiaminases.
In a live fish, the thiaminases are usually contained in specific compartments that prevent them from destroying thiamine in the host fish (which is why fish that contain thiaminases aren't necessarily suffering from thiamine deficiency themselves, and in fact they often contain higher levels of thiamine, presumably to compensate for possible degradation). But once the feeder fish is killed, the thiaminases are released and start to break down the thiamine in the tissue.
I imagine that most thiamine gets absorbed in the intestine, so if the ingested meal is exposed to high levels of thiaminases in the stomach the thiamine might be broken down before it gets a chance to be absorbed. So even though thiamine was initially present in the feeder, the fish isn't getting managing to get enough thiamine. This would also be a problem when feeding frozen feeders, because the thiaminases will have plenty of time to break down the thiamine when the feeders are defrosting.
However, as long as there is another source of thiamine in the diet that isn't being fed at the same time as the thiaminase-rich feeders the fish should be fine.
The analogous situation would apply to people - if you ate a lot of raw fish or ferns that were rich in thiaminases then that specific meal is potentially going to contain insufficient thiamine because it might get degraded in your stomach before getting absorbed. But as long as you consumed other sources of thiamine at other times you should be fine (a lot of nuts and seeds are usually a good source).
With regards to your other question, the temp required to destroy thiaminases varies depending on the organism that the thiaminase comes from, because different thiaminases have evolved to function at an optimal temperature for that organism. In the case of thiaminases derived from ferns, they starts to degrade at around 65oC so anything above that should be fine. I would guess thiaminase from fish would degrade at a lower temperature.
One thing to note about this though is that cooking the food should inactive the thiaminases, but it would probably also break down the thiamine itself so that's probably not all that useful. The trick would be to heat the food to destroy the thiaminases and then add some supplemental thiamine after it has cooled.
Incidentally, there is an additional level of complication which is that different species and individuals have different requirements for thiamine. In the case of the thyroid relationship that you mentioned, having hyperthyroidism can increase a persons' metabolism and this means that they need to consume more thiamine than normal to compensate.
Sorry for the long rambling post. Probably more than you wanted to know.