There was another post on this a while back. I don't believe there is any concern. Many of my clients have a NC-PAC system (big ones!) and it is an industry practice to use the table. The table is lowered a bit to accomodate OFC if required.
The caution for hydrogen is for the source, i.e.: tank, dewer, cylinder, hoses, regulators, etc. It is assumed you have your set-up in a well ventilated area and all equipment is installed and operating properly.
During CNC cutting of aluminum, disassociation of the water to hydrogen and oxygen can and does occur, just like we all remember doing in high school chemistry. If the cutting is done in an enclosed area without proper ventilation, hydrogen can accumulate in high areas (remember, hydrogen is lighter than air). You may also see some flames coming up around the plate being cut. This is not bad, as it indicates the hydrogen is being burned off. Anyway, adequate ventilation of the area is the secret to preventing hydrogen build-up. If you have the capability, gas analysis for hydrogen is a good idea to determine the effectiveness of your ventilation