Hi Bob,
Sorry I can't speak to the specific issue of an ES with nylon strings, but having used a number of diff Taylors into a system, I'd say there is a definite difference in timbre because of the woods, and that the ES does a good job of "translating" the wood choice when amp'd. For example, mahog b/s translates differently in the house than rw, and again maple ...as does a cedar top vs spruce. You can hear it; it's pretty obvious that each different wood combo is coming through the house system.
That said, I think there is a markedly smaller difference in body shape/size that translates through to the house tone. So if one were deciding between, say, spruce/rw among the GC, GA, and GS bodies, that is a much smaller (almost negligible, IMHO) tonal difference through the ES-into-house than comparing those guitars to a cedar/rw. Well, IMHO anyway. Sorry, but looks like you're going to have to buy the guitar that sounds better to your naked ears.

Hope that helps you.
Edward