The fact that they would consider replacing with longer nipples is not good:
1. Nipples are not spokes, and aren't intended to act as such.
2. Too short spokes = eventually nipple barrel and nipple head separation.
They should know better. Clearly they build wheels by habit and by winging it - not by any understanding of even the most basic wheel building science.
And I don't claim to be an expert at wheel building "science" though I do play one on BikeForums TV.
Recommendation: When it comes to custom wheel builds, find a new LBS.
=8-)
__________________
5000+ wheels built since 1984...
Disclaimer:
1. I do not claim to be an expert in bicycle mechanics despite my experience.
2. I like anyone will comment in other areas.
3. I do not own the preexisting concepts of DISH and ERD.
4. I will provide information as I always have to others that I believe will help them protect themselves from unscrupulous mechanics.
5. My all time favorite book is:
Kahane, Howard. Logic and Contemporary Rhetoric: The Use of Reason in Everyday Life