First of all. They don't have thousands. Not even close. The vast majority of Nintendo console games on NES and SNES are 3rd party. Nintendo averages about 1 game per franchise per console with a few notable exceptions but not very many.
Super Mario (not counting remasters) NES 3 SNES 1 N64 1 GameCube 1 Wii 2 Wii U 0 Switch 1
New Super Mario DS 1 Wii 1 3DS 1 Wii U 1 Switch 0
Mario Kart 1 on every system since SNES except Switch
Paper Mario N64 1 GameCube 1 Wii 1 Wii U 1 Switch 1
Zelda NES 2 SNES 1 Gameboy / GBC 1 (Oracles were not made by nintendo) N64 1 GBA 0 unless you count 4 swords (minish cap not Nintendo) DS 2 (gag and puke) GameCube 1 Wii 1 Wii U / Switch 1 (release same day)
Nintendo just doesn't make many games in their franchises. You'll find similar numbers for Metroid, animal crossing, star Fox, f-zero (last game on GameCube) smash, Mario&Luigi, etc.
I feel as though youre drastically missing the point.