Space dynamics are not that much deterministic. Gravity itself is kinda noisy (Earth isn't an ideal sphere with uniform density), there's the Moon, orbital decay (caused by drag from particles in low orbit, which is variable), solar radiation pressure (also variable), etc. Calculation of the dynamics will only give an approximate result, a prediction. They need constant measurement of the trajectories and frequent correction maneuvers (by ion engines). But yeah, I think that once the satellites accurately know each others trajectory, their movement shouldn't be a big issue for the lasers, as in the timespan of one laser connection it should be predictable with the required precision. And if both satellites would be on the same orbit, their relative movement should be ~0, so the laser beam ideally wouldn't move at all from the satellite's perspective, the angle would be constant.

Starlink sats do fly just low enough that they experience some mild atmospheric drag. Their next generation sats will fly even lower too. But it's certainly still in the range where simple computer models will be very accurate for at least a few hours out.