It depends on the page coding and subsequent pop ups page structure.
I recommend you learn to use the Network Console tab in your browser, filter against /b/ss/ and look at parameters captured. Look for activity map section.(often times its on destination page of where link clicks through to.) it will show you if coding needs to be addressed or if you have to use custom links...
If we're talking about a standard href with nothing fancy, it is very likely that it will be tracked in activity map. However, if you have custom coding, Activity map might not be sure how to handle it.
Pablo's answer of checking the debugger would be correct - bottom line is that every implementation is different, and the most sure-fire way to validate if activity map will work would be to test it directly.