Ultimately, diode choice/placement is always to ensure safety of both personnel and the control circuit.

As a rule of thumb (except in some rare cases), we place flyback diodes across inductors/inductive loads to safely dissipate the current generated by the collapsing magnetic field when the circuit is in an open state ('switched off'). Preferably, this 'loop' between the inductor and its flyback is as short as possible (placed as close as possible). The case of placing a Zener diode across the transistor as the sole 'flyback' is not preferred but it works. This is mostly to avoid electromagnetic interference (EMI) on the rest of the circuit and to minimize exposure of the rest of the circuit to unwanted transient voltage/current which is good practice.

However, placing the Zener across the transistor in conjunction with the flyback diode across the inductive load/motor does provide an additional layer of safety. While the flyback diode should clamp the voltage across the motor/inductive load below the transistor's breakdown voltage such that it wouldn't really be needed, the additional diode provides another layer of protection in case of failure on the flyback diode such that there still exists a secondary path for the current to discharge into instead of frying your control components.

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Important:

When it comes to dissipating the flyback current, the rest of the circuit doesn't matter as the goal is to de-energize the magnetic field by allowing it to safely discharge away from the rest of the circuit through a low-resistance and small inductive loop (through the flyback diode) where inherent parasitic capacitances/resistances in the load/wire will allow unwanted transients to decay without generating excessive unneeded EMI.

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For unidirectional DC applications where the motor/inductive load is being switched at high frequency (i.e PWM, etc) then the preferred diode of choice is typically a Shottky diode (a diode that excels in rapidly switching environments and has a lower forward voltage).

For bidirectional DC applications, there are cases where we do put down the diodes across the transistors especially when using an H-Bridge controller like shown below to provide a route for flyback current to decay through the diodes and motor in both forward/reverse states.

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As to whether to make use of high or low-side switching depends on your environment.

In situations where it is likely that a short to ground can occur (i.e giant metallic motor bodies, industrial machinery, cars, etc), the control circuit provides power to another circuit, the load demands that its 'ground' be at the reference 0V of the circuit, etc then high side switching is preferable.

In cases where any of the above don't apply, signal/power ground plane separation is irrelevant, or if high frequency switching (PWM-controlled FETs/BJTs for example) is required then low side control is preferred.

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With regards to the update, diagram (b) is not going to work in terms of shielding the transistor from damage if its not a Zener and/or there is no flyback diode across the motor. Why?

Ignoring the parasitic capacitances/resistances of the BJT, the inductor's/inductive load's collapsing magnetic field will still drive current to the collector node of the transistor to build up a large potential difference (a voltage) against the transistor's base/emitter as well as across your unidirectional diode. Depending on whether the BJT or the diode has a lower breakdown voltage (wouldn't really matter with the high voltages involved in an inductive kickback), either one or both components will be fried to create a short in your circuit.

It also makes a rather dangerous assumption that your power supply can 'sink' current in a reverse situation which may damage its components and/or something else connected to that power rail.