It's possible, but IMO, cyano is one of those things that is always there, it just shows up when conditions are right. So if you don't have it in your DT now, it's not highly likely you'll get it after the ATS is running. That being said, you don't really want to encourage it's growth anywhere in the system, so blocking light to the sump is a good idea.
There is always a chance, no matter what system you run, that you will have a cyano outbreak. It's not predictable, and I can't say I completely understand the mechanism behind it. I successfully battled cyano in one tank, but that tank was in the worst possible condition - N >800, P>5, only bio-ball filtration, not enough LR, no tank cleaning whatsoever in 3 years, old lamps, etc. I did it by attacking it from all angles - physical removal (including top layer of substrate), PWCs, removing rocks and scrubbing them, running a canister filter, Purigen, adding a skimmer, filter socks, and I'm sure I missed something. Eventually it just lost a foothold and I haven't seen it in a year.
Some have experienced cyano blooms after installing an Algae Scrubber, after it wipes out the DT algae and N and P are down, but if your scrubber is built and maintained properly, it's just a matter of time before cyano gets out-competed.
So the safest route is to not give it what it needs - light.