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to zero or not?

There is a slight difference in the tone. To me, though, the open strings are always a little brighter, so the metal fret can brighten it up even more. I like bone nuts myself. There are many great bass makers that use zero frets, so I guess it depends on your taste. If it's not a big deal you might want to try it and hear for yourself.
 
Forget the debate on tone, there is one cool thing about zero frets. I swap between piccolo tuning and BEAD on my Steinberger, same as I used to do on my old Kramer aluminum neck. Other than minimal bridge height and intonation adjustments, I am ready to go. I have never been able to swap that wide of a range of string gauges on a standard nut without recutting or filling it in.
 
I have basses with both zero frets and none, and I don't think it makes a difference in sound. CERTAINLY not as much difference as changing strings.

Not changing strings, but switching to a radically different gauge. A nut on a Fender style bass that is cut properly for a normal E-A-D-G tuning, usually will not work well with B-E-A-D tuning. The strings will not seat properly. Example, if you file the slot on an E string (.100 to .105 gauge) to fit a B string in the .125 to .130 range, great. But when going back to the standard E string the string will sit sloppy in the slot. And forget trying to use a .050 piccolo string in a slot cut for a .130 B string.

The is not as big of an issue on an angled headstock as it is on a non-angled headstock like a Fender, especially on the E and A strings. But it is still an issue in my experience.

A properly cut nut should match the gauge of strings being used. The zero fret approach is different in that the zero fret is the contact point for the string and any nut that may be used with a zero fret mearly acts as a guide for the string.