Confirmation or acknolwedgement?
To me, "you got it!" is primarily a confirmation of a request, not an acknowledgement of thanks.
The use of "thanks" in sentences that are actually requests ("e.g., I'll have a regular coffee, thanks") might make this unclear, but as a response to a simple statement of thanks, "you got it!" doesn't sound natural. My first ...
Yes, in the US “you got it!” is used as an informal reply to “thank you”. Even though it may sound a bit confusing, as the last commentator pointed out, the meaning behind it is similar to “sure thing” or “any time”. It is not a simple “you’re welcome” but more so “you are always welcome”, i.e. every time you need my help you will get it, it’s no bother.
"I will apply to" is not correct in this case.
You will "abide by" the terms and conditions or you "agree to" the terms and conditions.
An NDA is a binding legal agreement so it it correct to say something like:
"I have read, understood and agree to be bound by your Non-disclosure Agreement dated..."