Here's a recipe for output disaster: Set some type, and save it as EPS1. Import EPS1 into Adobe Illustrator, and make it part of a logo. Now save the art as EPS2, and import EPS2 into a QuarkXPress page.
Buzz! You lose! Nesting files inside other files demands intricate processing that confuses a RIP. The result can be substituted fonts, reflowed type, and gaping holes in your output.