One limitation in the 4000 series that has bitten me (I've got a 4162) is that you can't change the dutycycle of the square or pulse output without ending up with "gaps" in the output. I don't know if the 1000Z series is the same.
Not quite sure what you mean by 'gaps', but the DG4000 series enforces a minimum pulse width and rise/fall time based on the frequency of the waveform. I guess this is because of the limited amount of sample memory available, or limited processing power to generate samples on the fly. For example, a 1kHz pulse limits the minimum pulse width to 3.125us. There is a work around if you need shorter pulses - simply set the frequency to an arbitrarily high value, enabling a very short pulse width, then enable a 1 cycle burst and use the burst period to achieve the desired frequency. E.g. Configure a 10MHz, 8ns pulse, enable Burst at 1cycles, 1ms period - now you have a 1kHz pulse waveform with an 8ns width.
Achieving finer resolution of the duty cycle for a square wave can be achieved the same way by manipulating the frequency of the square wave and using the burst period to set the actual frequency.
Another limitation I've found with my DG4062 is that the external modulation inputs seem to be digitally sampled at about 8bit so the dynamic range isn't that great. A Tek AFG3000 seemed to work as if it were analogue in the same application (phase modulating a 1-10kHz sine wave)