Well, it does seem that Mini Nukes are more rare in FNV than in FO3; and personally I think that's a good thing. On my current run through FNV I believe I only bought one Fatman launcher from the Gun Runners and found one on the body of a dead Super Mutant Master (in poor condition) and maybe a total of 5-6 Mini Nukes at present time. In FO3 I was lobbing them away like candy (had a laugh with the MIRV too), but it just didn't feel right to find so many of them everywhere.
EDIT: Just checked the Wiki, and there are around 14 to be found/stolen for free in FNV, compared to around 70-74 in FO3 (98 with all addons). Guess that explains things

Greetz,
Milt