On ATS-34, the spots are probably black oxide left by exposure to something acidic or caustic (chemicals, salts, etc). ATS-34 is normally very rust-resistant, so it would take something fairly aggressive to stain it. Having said that, the bead-blast finish is probably the biggest issue, as many stainless blades finished that way have had issues with staining or rusting. The finish is much 'rougher' at a microscopic scale, and it tends to collect and hold stuff that contributes to corrosion, much more so than a satin or polished finish would hold onto. All that said, so long as the spots are actually black (not red or brown), it won't harm or pit the steel. I wouldn't worry about it.
Some Bar Keepers Friend powder, mixed to a paste with water and very gently scrubbed onto the isolated spots, would likely clean them up. Be careful not to leave the BKF on the steel longer than 30-60 seconds, as it's also acidic (oxalic acid), and it'll stain the steel if left in contact too long. Rinse it off very thoroughly under running water. If done quickly in this manner, it's also less likely to alter your bead-blast finish. Might test it on a less-conspicuous area first, to get a feel for how it'll react on the steel.
David