I think it totally depends upon the user and the knife. If you're of a larger size then a flipper might dig into you carrying IWB, but only a poorly designed one. There are many reasons to like a flipper. I like them mainly because (assuming a good design) they form an integral guard which will protect my hand; and they are the ultimate low-tech way to open a folder. I live in a VERY knife-phobic environment, and I like that I don't have any springs in my flippers to be confused with an automatic (like Kershaw AO often is). As an added bonus to this, there aren't any issues with springs fatiguing either. Just a nice way to open a knife.
That said, when I get my RJ Martin Devastator, it WILL have the (now) optional thumb-stud. I'm sorry, but a blade that can only be opened by a flipper is all but useless for me given my living environment. IMHO you almost HAVE to have an alternative method to open a flipper for those times when you're around NKPs. They get pissy enough when you have a knife in the first place without me having them scream either: "He's got a SWITCHBLADE!!!" or "Is that thing LEGAL?!?!?" My own lovely wife who is quite used to me playing with knives- while observing me breaking in a CRKT M-16 Special Forces knife- in fact made the comment about autos not being legal here.
Far as holes in the blade weakening it, well I suppose its somewhat true. I mean, you can hardly have MORE strength by having LESS material, but the difference would probably be miniscule at best. The pivot will most likely go before the blade does.