Aoi Art actually had a reasonably priced Morioka Miyaguchi daisho (900,000 yen) that I was almost going to buy back in Nov last year. I went down to the store, viewed the blades, and spoke to Tsurata-san about getting the daisho certified as such with NBTHK papers. He confirmed that as long as a katana and wakizashi were of the same smith with matching mei and nenki, NBTHK would paper them together on the same certificate.
I went ahead and reserved the daisho, and was preparing payment when Aoi realized that Mr. Miyaguchi was still alive at 92 years old, and was still taking commissions for swords! So I couldn't get the daisho papered, and didn't proceed with the purchase.
Therefore, it's apparently reasonably easy to get daisho NBTHK papers if you meet the conditions stated above, but you don't really see pre-shinshinto blades made as daisho.