How is a student perceived if he took more time to graduate?
Would he have any disadvantage as a PhD applicant?


Yes of course. But how big this disadvantage is, or if it is even relevant at all, depends on many factors:


country
field
courses taken (that might actually be an advantage!)
reason for the long time
was that long time used properly (e.g. to produce a really good Master Thesis)
other applicants
how common an A-Master is in your field/country/at your university
...


I would personally say that the disadvantage is not that big, but that is only my personal opinion, and chances are low that I will sit in your PhD admission committee...
I don't see how you would be able to get a general answer even when providing all these answers and I would suggest asking someone who knows your situation (e.g. your advisor, if you already have one).