Is there any disadvantage in pursuing a career course in VFX after B.E or B.Arch degree?

There is no disadvantage as such , only that may be your previous skills are not related to it. Yes , it depends on Be on which domain , if you are from IT background then it will surely be an added advantage.

There is never a disadvantage of any courses, however you need to be sure of the value it would be able to add to your career