Most forks are lowered incorrectly, which causes handling issues and potential clearance issues.. To do the job correctly, there is a spacer inside the leg above the valve body that limits the tube extension length. You add spacers to the stack to reduce the fork extended height. This also moves the compression stop down into the slider, to limit travel an equal amount. Raising the forks in the triple clamp is a hack. You still have full compression, which means the front wheel will travel fully upward but clearance above it will be reduced by the amount the forks are moved, which could potentially cause contact with the lower clamp, or in some cases the fork boots with the triple clamp. When you do it right, lowering a bike 1.5" reduces suspension travel by 1.5" as well, so that in full compression, the wheel and fender do not travel further than the original compressed limit.
The same applies to the rear shock. Lowering kits that just move the lower shock mount downward, effective raising the swingarm, are just a hack. The result is a full suspension travel rear suspension, now closer to the frame and bodywork by the amount lowered. The only proper way to lower the rear is to purchase a proper shock that is shorter in both extended and compression by the same amount. Lowering the rear by 1.5" then reduces rear travel by 1.5", just like the fork, so that the suspension in full compression maintains the original rear wheel clearance. On the R3, lowering the rear also increases the swingarm length a little, and puts the axle higher in relation to the counter sprocket, which will have an effect on how the bike squats under acceleration (more on a lowered bike).
There is another issue frequently ignored. When you drop the suspension, you reduce trail at the front wheel, since the wheel moves upward at the rake angle. This reduces steering effort, center feel, and ultimately stability at higher speeds. Under hard braking, when rake is lost due to fork compression and rear shock extension (pitching/rotating the chassis forward around its center of gravity), trail is diminished even further - and the result can be a rather nasty head shake - at the worst time, and unpredictably. On a light bike, neither are a good thing.
This is why lowering bikes is not really a good idea if it can be avoided. It initially reduces ground clearance, reduces suspension travel, and reduces trail on the front wheel. It is possible to work around the trail issue by lowering the rear somewhat more than the front, to impose additional rake to regain trail... but that's not something most backyard modifiers are prepared to work out, and beyond the expertise of the majority of dealers as well.
Yes, we all know that there are lots of improperly lowered R3's (and others) around, with satisfied owners. All I can say is that you don't really know whether there is an issue, until there is - at which point, the consequences of getting it all wrong can be a bit ugly.