Unless there's been a significant upgrade in pirate infrastructure, those 'motherships' are merely local dhows. I agree that the should be subject to search and, if resisting, destruction but that doesn't mean that they will shortly dry up and disappear. The coast is full of dhows. Finding the right ones won't be easy and if you sink a few, there are plenty more where those came from.
Actually, there's been a significant upgrade in the pirate infrastructure. Back in the '90s it was fishermen in their skiffs and dhows a few miles from shore. As they became more skilled, they kept some of the ships they captured. As they advanced into using freighters and trawlers, they were able to work farther from the shore. These days, attacks are occurring hundreds of miles off the coast. The mothership will launch two or three speedboats that work in concert to hijack a merchant ship. Unfortunately, international law keeps us from stopping and/or attacking these ships, even when they obviously have weapons and speedboats instead of fishing nets and legitimate cargo, unless they show hostile intent first. The one sunk by the Indian Navy actually thought it could successfully attack a naval vessel.
And RR...These are not a few amateurs. These are poor Somalis hired by the warlords who have been fighting over Somalia for the last fifteen years. The pirates have RPGs, NVGs, and other modern equipment. Somalia has 1,800 miles of coastline. If you really think that destroying a village is going to do anything to solve this problem, you need to stop watching so many John Wayne movies. We don't have knockout gas that works the way that you describe. Believe me when I say that if we did have it, we'd be using it right now. Of course, if you did understand anything about either Africa or Islam, you'd understand that sending naked women and children across the desert would almost certainly lead to some of them dying from exposure. You'd also understand how deeply offensive Muslims worldwide would consider the idea of naked women being turned out of their homes.
Yes, I have been to Africa. Yes, I do have some understanding of the effort and skills required for a coastal attack. No, these pirates are not all operating out of the same village, so destroying one won't have much effect. No, the masterminds behind the pirates are not living in these villages either, so killing the poor Somalis will only make them recruit other poor Somalis. Yes, I'm very well aware that surgical strikes only really exist in Clancy style novels. And yes, I do understand that you are inhabiting a fantasy world. But don't let me stop you.