Do universities mind study delay when reviewing your application? I have been getting good grades for the last 1.5 years for my bachelor (physics), therefore I have been considering applying to a more renowned university for my masters. 

Lately, I have also put more work in my honours programme because I really, really enjoy it - and I want to keep putting my time in it. However, the last couple of months I have noticed that is quite stressful to maintain my standards for grades while also putting time in honours, friends, fraternity, girlfriend, ... - it is so stressful I get really bad headaches when I do not relax enough.

Therefore, I am considering to follow one course less per quartile so I have more time to do other stuff, but can still maintain the grades. This means I will take 3.5 years to complete my bachelor, compared to the normal 3 years it takes.

Thus, my question; do universities take into account your study delay when reviewing your application?
Admissions committees care primarily about your grades and only to a very small degree do they care about how long it takes you to graduate. People have all sorts of reasons to not graduate in the fastest possible time -- most importantly having financial needs many students need to satisfy by working while being a student.

So no, there is really no need to worry about a semester more or less. Worry about your grades :-)