Power 4.5V Lego motor by 5V PSU, how?
In my opinion you are good to go.

.5V more for a dc brushed motor that normally accepts 4.5V is not an issue at all. That's a bit over 10% increase in voltage, that's not much. You can assume that the lego guy that designed the system choose a motor with a maximum voltage much higher than its normal operating voltage. If there's a cap inside it's probably (certainly) rated for much more than 4.5V

About the EM emissions/disturbance on the power lines remember that:


the Pi has its own filtering stage that is probably designed to handle much worse disturbances
the psu is so oversized that it would barely notice a change in load
there's plenty other disturbances going around coming from your pc


My advice is: try it out. It's not like you are going to blow up anything. Keep the motors on and see if they get hot (that is very unlikely), then sketch down a program that switches polarity (no off time) let's say once a second or so, and see if the pi is concerned about that. If something go wrong come back here and we can help you to design a filter circuit that can reduce the disturbances on the power lines.

I'd like to see the circuit you are using to power the relays from the Pi, that's because disturbances are much more like coming from there.

disclaimer
I think my advice applies here because it seems we are talking of a guy who wants to hack together a robot or something similar. If you want to design a reliable thing that will be produced you better choose carefully the motors and their power sources.