In general, while choosing the antenna locations the following considerations are taken into account:
- Obstruction of the signal by the aircraft (components).
- Structural issues like vibration and flutter.
In general, if the aircraft being operated from a towered airport is fitted with two radios, it is advisable to have the antenna for COM1 on top of the aircraft and COM2 on the bottom, with a separation of at-least one meter.
Also, usually, the top antenna is used in ground and the bottom antenna is used for air to ground communication as VHF (or UHF, for that matter) is line of sight. Note that it does not matter whether the COM1 antenna is on top or bottom; the top antenna is usually used for on-ground communication (sometimes, this doesn't work, as the tail plane might obstruct the signal). Another reason for using top antenna is that the bottom antenna could be damaged in case of hard landing.
As long as the antennae don't suffer from 'shadowing' of the aircraft, it can be located anywhere. A good example is the location of antennae in case of homebuilt aircraft from kits, where the both the antenna could be on top or bottom or even have a single antenna for the same model.
In the other extreme, the (avionics) manufacturer may prescribe a particular installation location for the antenna (usually for COM1 on top). Also, in some aircraft, the VHF radios will use both the upper and lower antenna. The signal is switched between the upper and lower antennas with coaxial relays, with the top antenna used while on ground, while the bottom one is used in air.
Also, the HF antenna is usually on the vertical tail and GPS antenna on top of the fuselage (for satellite signal reception). The antenna are mounted on the aircraft plane of symmetry or symmetrically to the either side of it (like Cessna 150).
For a short answer to your question, in general aviation aircraft, the location of com antenna is immaterial as long as there are no communication issues.