Depends where and how large the hole is compared to the tubing size. It can be readily done, and a thru-hole too as the tubing wall thickness isn't likely thick enough to tap threads in or use self-tapping bolts on.
If you drill it, either spot paint it or saturate a q-tip with paint and slather it on the exposed metal of the drilled holes.
The mentioned u-bolts would work. But they'll be unsightly and you'll have to deal with the projecting threaded ends sticking up above your wood deck.
If you drill thru the tubing, I'd suggest using cap-head screws and fender washers as a way to have a secure bolt-down on the wood surface while simultaneously having smooth rounded hardware for any cargo to rub on. On the bottom side, use a washer that's as wide as the tubing - is the tubing flat / square? or rounded?
Use a springloaded punch and a smaller drill bit to make your initial holes, you'll have better control and accuracy and will be far less likely to have the bit wander all over tearing up the powdercoat? finish.