I have heard/read two somewhat conflicting stories about the holsters.
First; from a Bob Guernsey interview in which he relates the story of putting together the first paintball gear package for sale to people. It consisted of a Nelson 007 (which the Nelson folks would barely discount for him), a hat, shop goggles, a couple of cardboard tubes of paint, a handful of 12g's and, finally, this holster.
In the interview, he indicates that he found someone who would make him holsters (or already had made) that were perfect for the Nellies. In fact, he stated that some large proportion of the $300 price for the paintball package had to go for these very expensive leather holsters.
Second story; Reading one of those factory tour/product reviews from an old APG (or other, I have not refound it yet), I found a mention of the holster. Nelson claimed that it had contracted for the holster as part of the initial product offering of the Nelspot to farmers/loggers, etc.
Also, those full color ads featuring Nelson products that came out in the late 80's, early 90's (there is a pic of it at VR) shows the exact same style of leather holster in the arrangement of all the products.
Did Bob Guernsey have it designed for the Nellie, or did Nelson?
I guess it doesn't really matter as your question was about whether it was made for the gun or existing when the gun was invented.
Best I can tell you is that the (bolt-action) Nellies fit into these holsters perfectly and as if they were made for the gun.
Final note; I once bought a High Standard .22 revolver that came with an identical leather holster as the Nellies had. Thing is, the holster fit the HS in exactly the same perfect way.
Go figure. Another Nelson mystery for us to solve.