"I really dont see the need for permission, If they are in Thai waters."
Translation: the Thai government (or businesses) don't want to PAY for the retrieval of these mini-subs. Better to stick the "country of origin" with the bill. These are British wrecks, probably not worth much as salvage, sitting in Thai territorial waters. The Brits have, in effect, "littered" in Thailand. It's only right to ask them to clean the mess up,and pay for it, too.
They may also still have "live" ordinance aboard, which while submerged in salt water for sixty years, might still go "boom" when you least expect it.
I disagree. Without knowing more details, it is hard to say, but here is my take. Whoever is in charge on the Thai side is not sure of the legal situation. If he approves something that could come back to haunt him, he is in major trouble. He is not going to risk his career, or chance of promotion, by doing something that will piss off the UK.
The other possible answer is whoever is in charge on the Thai side is making it difficult because he is looking for a bribe. He is throwing up artificial obstacles in order to get it. This is very common in Thailand and I have run into it quite often here.