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Depending on how much you lower, it may be difficult to get it on some alignment racks. I couldn't get my car on the rack at the Goodyear store on Pendelton Pike (where I had my previous cars done)...I have Raftracer down in Cinci do mine, but I do understand that Matt's alignment on Capitol Ave has a alignment pit that you can drive over that can work with really low cars. Haven't used them, but it may be something to look into.
To answer your original question, Nope, no problems at all, 50K+ miles since I lowered her.
As far as alignments go, virtually every Vette I've seen coming from the factory has the alignment off. Sometimes not much, sometimes quite a bit. So, getting an alignment done is a good idea anyway, if you haven't done it yet.
Some racks mine will go on, most it won't without some lumber to get it up on the ramps.