Bob,
Shortening the wires in principle is ok.
Now for the issues.
Some motors--like the Scorpion for example, bring out the actual windings to the connector. Which means that if you cut them, you need to strip off the enamel coating. Again not a big deal---if one winding turn was one wire. But actually Scorpion uses many strands of fine wire in each turn, so the net result in this case is that you will have a very large number of enameled fine wires to strip--and you might not be sure if you really stripped off the enamel on every tiny strand. So for example on a Scorpion 3020-890, each wind is actually 14 strands of 30 gauge wire, and each connector has two phases worth, so there would be 28 fine wires to each connector that you would need to strip. And remember there are 3 connectors!
There is a technique to strip these things---apparently a melted (by heat) aspirin will dissolve the enamel. The fumes are claimed to be pretty acrid, so don't breathe the fumes!
However if your motor has normal insulated flexible wire coming out to the connector, then you are home free. Feel free to cut it and the ESC leads as short as you want!