Just to add to what Joojaa said.
Maya of course has to calculate all the connections you make, so having an excessive amount of connections will slow down your performance. But you should't worry about this at the expense of making your charater, or whatever you are building, work the way it needs to. You should connect as many nodes as you need to for whatever you are building, and not worry about a specific amount as being too many.
In a lot of cases it is good use constraints instead of parenting as it gives you an extra level of control and allows you to separate and group nodes in the scene hierarchy. A simple example would be, constraining instead of parenting rigid objects to a skeleton. That way you can keep all the character geo grouped together, separate from the rig.
Parenting IK's under controllers is good, keep doign that. All that stuff should be hidden from the animator. don't let them touch the joints or IK's or anything else directly. just give them control curves that control everything with direct connections, expressions, or set driven keys etc. Another benefit is that if you turn the selection mask to just curves you can select all the animation controllers easily.