Actually this is tried tested and patented technology that has been used for oil well blow out containment and separation.

Really? Didn't know that. It's really cheap and simple. If I had the money, I'd immediately go for it...

However capturing too much of it might upset some balance within the Earth that we do not know about right now.

It's not about deep deposits. According to the researchers, the methane ice which would go into the atmosphere with 1°C higher water temperature is right at the surface.

However methane and other hydrocarbons are naturally and constantly produced.

Totally. On top, it would also reduce the climate emissions by a margin as methane is ~25 times as bad as CO2, if you believe the climate crowd.