multiplex multiple photodiodes to one transimpedance amp
1) In the case of a photodiode with very low current output, the effect of the 60ohms series resistance of the HC4051 multiplexer will be negligible.

2) A long distance between the photodiode and amplifier increases the capacitance of that node. That may make your amplifier unstable if it has no additional capacitance across its feedback resistor, add a few pFs here to make sure it's stable.

It also gives greater opportunity for pickup of stray signals on that very sensitive node, which you can avoid with shielded cable.