The first question would be: "...a difference compared to what?"
Most camera lenses have been multicoated for decades now. Before that (from around the '50s to the '70s) they were single coated. Before that, most were un-coated.
- Uncoated lenses typically lose around 4-8% to reflection.
- Single-coated lenses lose around 2-4% to reflection.
- Multicoated lenses lose around 0.5-1% to reflection.
- Nanocoated/SWC lenses lose around 0.05-0.1% to reflection.
Literature from both Nikon and Canon often compares transmission with their new coatings to transmission of lenses with no coatings at all. Although technically accurate, I find this disingenuous at best, carrying an implication of a much larger improvement over existing technology than is even close to real, by comparing to lens designs from the 1950s (or earlier).
I hasten to add, as well, that achieving a transmittance of 99% isn't exactly new or earth-shaking. Good multicoated lenses have achieved transmittance around 99 to 99.5% for decades now (and there does seem to be a clear trend for improvement over time, so I'd guess current coatings are mostly closer to the top end of that range than the bottom).
In theory, if you applied nanocoating/SWC to every lens element, a design with lots of elements could reduce reflection by quite a large margin. In reality, it's only applied to a few surfaces (e.g., 2 to 4 out of designs with around 11 to 13 elements--and frequently only to one surface of an element).
There are a few potential advantages, such as allowing a lens design that would otherwise produce unacceptable levels of flare/ghosting1, but would be acceptable with good enough coatings. At least to my knowledge, that's purely theoretical though.
Looking specifically at flare: the lenses to which these coatings are being applied make no sense to me at all. Flare and ghosting are real problems with wide angle primes and (especially) short zooms. The lenses you can get with these coatings are almost exclusively long primes.
At least in my use, even with a 70-200/2.8, flare is rarely a problem. With 300mm or longer...I'm pretty sure every picture I've had to discard due to flare or ghosting problems could be counted on one hand with fingers left over.
Bottom line: I can see ways this technology could be a good thing, but as it's often currently being applied, it strikes me as unlikely to produce any significant improvement.
1. I can certainly think of a few specific lenses I'd love to see re-introduced with such coatings applied--great in other ways, but major problems with flare/ghosting.