Variable emission is one of the defining characteristic of active galactic nuclei (AGN). While providing precious information on the nature and physics of the sources, variability is often challenging to observe with time- and field-of-view-limited astronomical observatories such as Imaging Atmospheric Cherenkov Telescopes (IACTs). In this work, we address two questions relevant for the observation of sources characterized by AGN-like variability: what is the most time-efficient way to detect such sources, and what is the observational bias that can be introduced by the choice of the observing strategy when conducting blind surveys of the sky. Different observing strategies are evaluated using simulated light curves and realistic instrument response functions of the Cherenkov Telescope Array (CTA), a future gamma-ray observatory. We show that strategies that makes use of very small observing windows, spread over large periods of time, allows for a faster detection of the source, and are less influenced by the variability properties of the sources, as compared to strategies that concentrate the observing time in a small number of large observing windows. Although derived using CTA as an example, our conclusions are conceptually valid for any IACTs facility, and in general, to all observatories with small field of view and limited duty cycle.