LLoyd J's answer is basically correct:
If you have the pcb, it makes things much more tidy.
Also, if you run a high current output wire close to a low voltage input, there can be oscillation and ghost notes. Avoiding this by proper routing of wires is called "lead dress" and isn't too difficult if you apply a little thought.
This looks like a simple guitar overdrive pedal. I love this problem because this is what I do!
I build guitar amps that are point to point wired. I do this because point to point is extremely durable compared to pcb. Printed circuit boards can develop cracks in the "traces" and can be difficult, if not impossible to repair. Hand wired amps and radios from 60 years ago are still functional and repairable.
An effects pedal, properly constructed, doesn't have the same vibration problems as a guitar amp or radio with it's own speaker in the cabinet, so this isn't as much of a consderation.
Here's a tip: use some sort of support, either an eyelet board or a turret board to mount the components. This will support them and keep them from banging around in your enclosure.
Short answer: wire your pedal either way. With a little homework it shouldn't matter!