No, TableNinja II was written from scratch and in no way uses AutoHotkey. It was built from the ground up and because of this TableNinja II is faster, more versatile, more user friendly, and more stable than most AutoHotkey scripts.
To use TableNinja II with a joystick you will need to download and use a third party program such as Xpadder®. TableNinja II does not directly read joystick input, but this program will convert your joystick input into keyboard or mouse commands which TableNinja II can then assign to hotkeys.
We try to make TableNinja II compatible with scripts and other programs when possible. However, there may be issues when using other programs, particularly ones that interact with poker site tables. If you are running other programs or scripts with TableNinja II and you find a feature does not work properly please try and turn off your other programs and see if you still have the same problem.
When you are the first to bet on a given street the pot-size is simply the total amount bet on all previous streets. In situations where someone else has bet in front of you TableNinja II calculates a pot-percentage bet as the amount of chips that have been bet prior to your action plus half of a minimum raise times the specified percentage, plus half of a minimum raise.
For example, if you are first to act on the flop and the pot is 1000 and 80% pot bet would 800. As a second example, if the small blind and the big blind post the blinds and two players limp an 80% pot sized bet would be 4.6 big blinds. That's 80% of 4.5 big blinds plus one additional big blind.