Are you sure the traditional MacOS paths really work?
Anyway, I would focus on what changed last Wednesday?
Did the server reboot or something?
I wonder if you have an administrative user mount the volume first, does it help?
(Also, I assume you aware that Adobe's licensing requires you to have a seperate InDesign license for each individual user who might access InDesign on your Aqua Connect server, not the number of concurrent users, and not one. See section 3.5 of the first link at http://www.adobe.com/devnet/indesign/documentation.html#citrix which of course is written for Citrix.)
The Aqua Connect server is a small, yet important, part of our production (so yes, we're properly licensed).
Generally, pages worked on through our multiple-use server are then passed to others to work on. These other users operate individual workstations. A requirement of this workflow is that the Aqua Connect server use the same paths and links as our other users do. Our non-remote users are happily linking away without this issue, as is the initially-connected remote user.
The server was rebooted on Wednesday as we end up doing about once a week. No other changes were made (as far as I can tell, of course).
I've found that no matter what user mounts an AFP/SMB volume (even root), other users cannot access its contents. The Computer window in Finder shows each mounted instance of each sharepoint, but only one of each share for each user can actually be opened by that user. This has been the case since at least Leopard (if not earlier).
Just an idea. Have you tried the free companion product mappable file-system from AquaConnect to give each user of your system a different physical location of your root-folder-structure?