I think it is 2), or possibly 3) (a combination of 1+2) - She was looking at her watch for the time as was bored, and also made sure the other person saw this to communicate non-verbally
there is definitely the element of 2) with 'pointedly' in that sentence
In other contexts not always though - pointedly to me just means deliberately and often to be seen to be doing something.
For another example I might say "I pointedly went to the shop late in the day" in the context of - "...as I wanted to go when the products were on sale" - this use does not have this overtone of 'attitude' or to be seen to be doing something - the word pointedly only highlights that this part is important/particularly deliberate ('pointing' at it)
hope this makes sense