I assume the "runes" was a typo there and you meant "how many runs you do". In that case, tecnically yes. In theory, having 250% mf would require more runs on avg than 400% mf. And no, the % doesn't limit you from not getting certain drops... that's all about ilvl and clvl.
However... I have HEARD that the % can affect what magical types drop most often. I don't remember what it is exactly, so here's an example. Again, I'm making up these ranges as an example...
100% - 199% mf = mostly set items will drop
200% - 299% mf = mostly rare items will drop
300% - 399% mf = mostly unique items will drop
400% - xxx% mf = mostlly magic items will drop
In my experience, more mf doesn't equal more unique drops... so I believe this rumor to be true. My opinion is that right around 300% is fine.