I agree Nadal isnt yet definitely over Sampras. Just probably over him. I do think even today most would now rank Nadal above Pete, but it is still within debate for now all the same. I agree he would need 2 slams to be beyond any doubt over him.
The thing about the time at #1 is Sampras for much of his time at #1 had less points than Nadal collected in being #2 behind either Federer or Djokovic. There are different veins to talk about quality of competition, but in the aspect of a singular great rival who produced a consistently extremely high level year round, Sampras by far had it easiest. Replace Sampras with Nadal, Nadal of 2005-2013 put into 1993-2001 would probably have been year end #1 every year except maybe 2012 (2000) due to only playing about half the year. I guess Agassi in 1995 would be close with Nadal of 2007 too, but Agassi's whole year was based around hard courts, even more than a typical Nadal year is based around clay. Even if Nadal didnt fare well at Wimbledon under 90s conditions, his massive clay points totals and consistency the rest of the year would easily make him #1 over most of the #2s of those years- Stich (1993), Agassi (1994, which he got too despite being World #20 close to the U.S Open), Chang (1996 and 1997), Rios (1998 ), Kafelnikov (1999). I know these competition arguments are a fuzzy area, but this isnt really that as so much an issue of performance. Nadal's performance and production in most of his #2 years was not inferior to what Sampras was producing in his #1 years, in addition to what Nadal produced in his times at #1.