The short answer is yes it does.
Certainly I discovered on my Sony HS-50 that if you use the lens shift, it causes the pixels to go very slightly out of alignment from the different panels. In the case of my projector which is mounted high up, I thought I had misaligned panels as I had a blue upper edge on any hard white lines e.g. credits, or the net cord in the film 'Wimbledon' caused by about 1.5 pixels of blue panel projecting above the others.
I thought I would try and get another projector and see if it had better alignment, so when UrbanT sold his HS-50 for a very attractive price, I thought 'What the hell' He assured me he could see no blue edge (or any other colour) that he could tell, so we conlcuded the deal and he shipped it to me.
I changed the projectors over, and hey presto, no blue edge.....
Until I used the lens shift to bring the picture down onto my screen just as my projector was set up, then the blue misalignment appeared just the same.
I then experimented with adjusting the lens shift of both machines and sure enough, the further the lens shift is applied, the further the blue pixels creep out of place.
I should point out that this is a very minor effect and many people possibly wouldn't notice it, but it is there and I do!
I wonder if this effect is caused by the different wavelengths of light (esp Blue) being diffracted by differeing amounts as the lens shift causes the light path to hit the lens at an increasingly oblique angle. If this is so then I would think that the same effect will be present to a greater or lesser extent on every projector that has a lens shift feature.
It's certainly worth mentioning that this is much less of an issue compared to using keystone correction which really does affect the picture.
Hope this long-winded reply helps!
So yes, the lens shift definately affects the picture quality, but by nothing like the degree