How come there are long pauses with weapons firing in VATS, does VATS nullify the Fast Shot Perk? If so I would have never gotten it...

.....

i dont think speed is the benefit, i think it is AP cost, while you are more inaccurate.

So, just in VATS instead of speed you get more APs? You shoot much faster when not in VATS...

Can someone confirm this for sure?

Here''s how Fast Shot works in VATS it lowers the AP cost by 20% so 30AP is 24AP.
It also lowers your accuracy by a similar percentage so while you might have seen 95% you instead see 76%

Fast shot reduces your AP cost and make you fire 20% faster free hand. And it increases your spread by 20% and reduces vats accuracy by 20%. However, because spread is used in VATS accuracy it actually reduces your accuracy a lot more then 20% when used at medium range. If you only like to use VATS up close and personal and perfer to free fire then Fast Shot is a pretty strong trait.

This thread lists out a lot of the trade offs involved.

http://www.gamesas.com/index.php?/topic/1186326-fast-shot-or-trigger-discipline/