Depends on the simulation, IMHO. If we (or our simulators) were to simulate the universe using space/time coordinates (i.e. "grid" and "ticks"), then I can imagine a plausible way of communication by creating unphysical objects - e.g. perfectly rigid letters with zero gravitational but infinite inertial mass. Though they might get the scale wrong - there could be a whole encyclopedia embedded inside a pebble somewhere in Earth's crust, or the Boötes void is a dot over an i.

If, however, the simulation is neither time nor space based - e.g. the universe appears inside Fourier transform of some simulation parameters, then not only intelligent agents, but even large scale activities inside the simulation might go unnoticed by the simulators. Similarly signals being sent into the simulation could remain unnoticed by the inhabitants.