Do the fruits in one piece have a limit based on the user vs victim strength? Could someone like Sugar just sneak up on Big Mom or Kaido and turn them into a toy?
Probably. No one besides Oda knows but it is likely.
There are limits to be abilities of some devil fruit powers: Bartholomew can only make a barrier of a certain size; Buggy can't levetate his feet; Even Luffy can only stretch 72 Gomu Gomu's before he starts bleeding and risk ripping according to Oda. (Of course that is due to the first SBS. These, while canon, are more humorous than anything. Gomu Gomu's is not a specific unit of measure.)
There are, however, no shown limits (so far) to Sugar's ability related to the size or power of the victim. Sugar used her power on many strong opponents with ease.
There is a running theme in One Piece of weak people being surprising strong in the right battle. Ussop beat Sugar and Perona when either could probably beat Luffy. Mr. 3 was indispesible in beating Magellan and rescueing Ace. Buggy held is own (sort of) against Mihawk.
Sugar, or someone similar, being able to turn a Yonko into a toy is not impossible based on how powers work and would fit well into the themes of the show.
There is, however, a theme of baddies looking beatable and then suddenly becoming far more intimidating. If Sugar touches a Yonko, expect something insane like Blackbeard countering the fruit with a hitherto unknown ability, a small toy Shanks defeating Sugar and her mooks itself, or a toy Big Mom/Kaido being even more baddass and imposing than the real thing.