It'd depend on how you define 'small.' If you're thinking about a miniature SSK with a hull length of 20-30 m, then no, it wouldn't be feasible. Even if Pakistan can design its own submarine, there are a lot of high fixed costs due to the need to import steel and propulsion, to say the least. The PN would rather put those resources towards a SWAT submarine to defend coastal waters than special mission applications.
However, if you're looking at a AUV-sized vessel of a hull length of 3-5 m, then yes I think it might be worth pursuing. But bear in mind you'll have challenges with power, cooling, propulsion, etc at that level as well. It's still worth studying though, for sure.