Will flash gels affect the output of the flash? It seems that your are diffusing it to some extent and would need to compensate for it.
Yes. It depends upon the gel, of course. A full CTO will effect the light coming form the flash more than 1/4 CTO. Do you need to compensate for it? TTL flash will automatically measure the output coming from the flash and adjust according, so no. If you're using the flash in manual mode then yes, you will need to compensate for it.
Very little diffusion happens, which is why gels look clear and not cloudy, but gels absorb certain frequencies of light, so the total output is reduced.
If your camera and flash support TTL metering, then the camera should compensate for the light loss however unless the camera has RGB metering it can't compensate properly and may require you dial in some flash exposure compensation, but only with very strong gels.