Is it safe to exceed an LED max current when ON time is less than 100%?
The datasheet will have this information. Some LEDs that can only handle 20mA continuous are spec'd for very brief pulses of a much higher current. You would have to specify the PWM frequency to be able to look up the answer to this question in a datasheet.

For one particular product, the CREE CLV1A RGB LED, you may drive red at 50 mA continuous or with a 200 mA pulse (pulse width ≤0.1 msec, duty ≤1/10), and blue and green at half that current. It's all in the datasheet. You can also see that there is a diminishing return as the relative luminuous intensity vs. forward current is not linear at high currents.

I think you should not worry about the brightness loss from driving your LEDs at a 50% duty cycle at the maximum continuously rated current. IIRC the eye has a non-linear response to brightness and they will appear somewhat brighter than half as bright, and you won't destroy your LEDs if you screw up the PWM.