On an experimental aircraft engine does the mag have to be repaired at a certified shop or can you send it to a cheaper automobile mag shop?

Car mechanics will not have an idea what a "mag" is.  The "mags" that they know is the part that you install the tire on.

Legally, anybody can work on them if they're going on an experimental... but no automotive shop would have  the required special tools or documentation.  Having them rebuilt by anybody other than an aircraft mag shop will add nothing to their value  and likely would REDUCE their  value.  There are no "automobile mag shops", because modern automobiles don't use magnetos.

Edit, I said MODERN cars don't use magnetos, and any shop that works on antique car magnetos still won't have the special tools and knowledge to work on an aircraft mag.