Several coronagraph designs have been proposed over the last two decades to directly image exoplanets. Among these designs, vector vortex coronagraphs provide theoretically perfect starlight cancellation along with small inner working angles when deployed on telescopes with unobstructed pupils. However, current and planned space missions and ground-based extremely large telescopes present complex pupil geometries, including large central obscurations caused by secondary mirrors, that prevent vortex coronagraphs from rejecting on-axis sources entirely. Recent solutions combining the vortex phase mask with a ring-apodized pupil have been proposed to circumvent this issue, but provide a limited throughput for vortex charges > 2. We present pupil plane apodizations for charge 2, 4, and 6 vector vortex coronagraphs that compensate for pupil geometries with circularly symmetric central obstructions caused by on-axis secondary mirrors. These apodizations are derived analytically and allow vortex coronagraphs to retain theoretically perfect nulling in the presence of obstructed pupils. For a charge 4 vortex, we design polynomial apodization functions assuming a greyscale apodizing filter that represent a substantial gain in throughput over the ring-apodized vortex coronagraph design, while for a charge 6 vortex, we design polynomial apodized vortex coronagraphs that have 70% total energy throughput for the entire range of central obscuration sizes studied. We propose methods for optimizing apodizations produced with either greyscale apodizing filters or shaped mirrors. We conclude by demonstrating how this design may be combined with apodizations numerically optimized for struts and primary mirror segment gaps to design terrestrial exoplanet imagers for complex pupils.