You can't wrap over rust, it'll be extremely obvious if there's any imperfections under the vinyl since it's so thin. If you wrap over lacquer peel you can plainly see it. So you'll be able to see if there's any problems with the body work. Like someone said it could have a different coloured wing or something..but it wouldn't concern me if I was buying. I'd be buying the car 'cos I like the wrap.
In terms of value it can easily affect it. Just a simple matte black wrap done well could quite easily not damage the value and would maybe push the value up slightly to the right buyer, but if you start putting tacky stickers everywhere and adding flames from the wheel arches then yes, it's going to drastically affect the value.
Basically, you can wrap a car to look after the already pristine bodywork - you can remove the wrap and be left with your brilliant paintwork.
Like with everything though, you get what you pay for. Your mate who buys his vinyl off of eBay who charges £100 and a beer down the pub won't do a decent job - a proper fitter will charge a lot more but you'll have much more chance of the vinyl not falling off and coming out of recesses a month down the line after a heavy frost.
Do it do it do it