All my personal games have replacement boards in them I can't see them affecting value unless its a Kiss or playboy etc being sold to collector. If selling to the home market all new boards sound way better than 40 year old ones
Replacement boards are usually improvements on the originals as well as replacements for old and troublesome boards. Unless your SD board has had major damage - such as burn holes where the Driver transistors are, then it is repairable.
KISS & Playboy are games where you would need to have very clean, updated and original boards. I have put aside the Homepin CPU boards for this purpose. They are faithful to the original, but they are reliable.