Can spending too much time in bed cause muscle deconditioning? i used to live a very active lifestyle but last 3 months nothing i get body aches...

Yes: Atrophy: the loss of muscle mass and/or function is common with prolonged bedrest. The old adage "if you don't use it, you will lose it" does have merit. Get better soon.

Yes, but...: Deconditioning can certainly be caused by spending too much time in bed, yes. I would be more concerned, however, about why a 21-year-old is having the body aches and is needing to spend so much time in bed. I would certainly consider talking to a primary care doctor about these complaints as they can be sign of a medical condition.