If you burn from the cue sheet rather than the ccd file the sub-code information will be lost.
Whether or not the copy cd will work will depend upon whether or not the sub-code info was necessary.
For example, if the relevant copy protection is safedisc, the sub-code info is irrelevant. Indeed, for safedisc versions from 2.8x to 3.10, one of the most reliable ways to make a working back-up copy, assuming that you had capable hardware, was to read the disc with CloneCD with cue and then burn from the cue with fireburner.
On the other hand, if the copy protection is an older form of securom or if you're trying to copy a karaoke cd, the sub-code info is essential and you won't be able to make a working copy by simply burning from the cue. It will be necessary to burn from the ccd control file with an app that can handle ccd images (obviously CloneCD itself can do so, alcohol can do so too, and possibly CD-DVD Mate can though I can't be sure as I haven't used that program for some years).