Tim Inman: Let's go in reverse order on this one: If your planer knives are so dull they are creating heat that could melt glue, stop planing and sharpen! Good sharp knives cut, not burn. Unless you're just ploughing off big wads of uncleaned glue left laying on the surface of the wood, then, "No," the glue will not clog up the planer. Now for the most important question. The glue should be dry before planing. So should the wood around it. If your glue is water-based (yellow, white, hide, etc.) then the wood surfaces near it have taken on extra moisture, and they have swollen. If you plane before the wood is back to normal dryness, you will cut off a little excess wood near the glue line. It will be nice and flat when you plane, but a few days later, you will notice that the wood has shrunk back. This leaves sunken areas along the glue line. So wait until the wood is dry before planing glued boards.

Chris Marshall: As a general practice, I scrape and scrub off all of the excess glue while it is still curing, so lumps and bumps of dried glue never run through my planer. What's left is just thin glue lines, so really a negligible amount of cured glue actually contacts the planer knives. As Tim says, let the glue cure, clean off the excess and then plane to your heart's content.