Non-isolated DC-DC converter for power supply and equipment at remote location (on top of a tower)
Is a non-isolated (shared ground) topology like this is problematic
for this use case? Should I use an isolated topology instead (flyback
with transformer?)

Not necessarily, but any EMI that induces currents into the OV line or -48V line will make the DC to DC converter in remote equipment box susceptible to the EMI. The other problem from the looks of the diagram the 0V ground and the -48V are also in a loop which has the potential to generate very high currents in the event of a nearby lightning strike.

How would a lightning strike (on top of the tower) affect remote
equipment and ground-level power supply if this topology is used?

In the event of a lightning strike, the very large current (100's of A) would flow through the lightning cable, which would generate a very large magnetic field. This would couple into any conductor following the same path and generate a smaller current on each cable.
Any loops on cables would capture and magnetic energy and the loop would generate a current (orange loop current)
In addition the sudden change of electric field would generate a large voltage change on the remote equipment box (green capacitance)

The remote equipment box could see thousands of volts (should be shielded) and the terminals could also see transient events lasting around 200us. This voltage could be high (such as ±2kV)  could be common or differential (seen on one terminal such as the -48V or both -48V and 0V at the same time)

Source: (pg 560) Electromagnetic Compatibility Engineering. Author(s):. Henry W. Ott.
I don't see any suppression circuitry on the DC to DC converter. I suspect that a 2kV spike would be outside of its specs. I would consider using isolation. This would break the ground loop and using a transformer does two things:

supresses differential noise
Transformers can be mad to saturate to limit energy moving into your device, suppression diodes after the transformer can then be used to suppress any high voltages.


If a grounding cable at tower that connecting busbar to ground somehow
disconnected, what risk exposed to remote equipment and ground-level
power supply?

No grounding cable would eliminate one of the ground loops, but lower the ability of the grounding system to keep the electronics at earth potential.

If a grounding cable connecting busbar to busbar somehow disconnected,
what risk exposed to remote equipment and ground-level power supply

The current from the -48V rail would be shunted to ground and the ground impedance would increase. Any potentials generated between grounds would be seen by the electronics.