Looking for some experience from the field -
The rack I manage has two zero-U vertical PDU's supplied by the datacenter. They have fitted one on each side (one on the left, one on the right). The rack appears designed so it can also accomodate having both PDU's mounted on one side. In our case the vast majority of equipment has the PSU's on the left hand side, so at face value it would make more sense to have both PDU's on the left, enabling a short tidy cable run.
Is there a big downside to having both PDU's on one side, or is the choice pretty arbitrary?
It depends... You should post the brands of the equipment involved.
For me, if it's a co-location facility, I'll take the lead of what the facility's staff recommend. They're the ones who need to provision power and energize the PDU's.
Also see: What to look for in a server rack?
For the datacenters I deal with, I usually mount both Zero-U PDUs on the right ride of the rack and use 1ft/2ft cables.