Yes.
The "unit of measure" roughly determines the denominator and hence the precision in the estimate of the mean (here, the click through rate).
Impressions vs users randomized is a great example. Imagine you randomized users to two arms for an experiment. One user in one fo the groups just LOVES clicking your ad.
If your "unit of measure" was the impression, you would have to count each click from this user as an affirmative outcome.
If your "unit of measure" was the individual user, then you see the user clicked at least once and you're done. (Actually, there is some more nuance here. You would either want to measure the outcome of the user's first time seeing the variant if possible or else a) measure the time to the outcome, if it happens, using a model which can account for censoring, or b) define a period of time under which the outcome can possibly occur. That is just some flavour though, not really important to what we are discussing).
Clearly, the expected outcome and its variance depend on the unit. So yes, it matters, and it matters quite a lot.