Is this the flickering effect in NES games?
I don't think so, at least usually.
The problem is that old consoles had strange limitations. Such as a maximum number of sprites on a given scanline (8 on NES, 10 on GB IIRC, a bit more on SNES). When there's too many sprites horizontally aligned, some of them would disappear. It's difficult to ensure that there's always 8 sprites or less on a given scanline, though, especially with some games.
To avoid sprites completely disappearing for long amount of time, some games cycle the order of the sprites, so that the ones disappearing aren't always the same ones. Thus the flickering.
That being said, a late updating of the sprites position registers can cause flikering, too, so in very very rare cases, it could be a framerate issue. But that's not the main reason.
I think a lot of NES games had the flickering sprite issues. I definitely remember there being slowdown in Megaman 3 at the least.
A lot of NES games flicker, indeed, because of the 8-sprites limit, which is quite low.
But that usually hasn't anything to do with slowdowns (although flicker appear when there's too many sprites in a single scanlines, and slowdowns when there's too many sprites on screen, so the two can often happen at the same time)