"/etc/hildon/theme" is a symlink to whatever theme is currently selected.

Yes I find this tricky too.
[Background Info] From what I know, icons are located in "/opt/usr/share/icons/".The default ones are under the "hicolor" folder.If a theme uses its own icons then they will be under their respective theme directory in this icons folder (further categorized by their size).
The desktop application icons are 48x48.for eg "/opt/usr/share/icons/hicolor/48x48/hildon/" is for default theme.This is where icons for default applications (phone,contacts etc) and for (some) apps are located.
What I think is done here is,icons are first searched under "../icons/theme-name/".If they are found here they are loaded.If not then icons from "../icons/hicolor/" are loaded.In case they are missing here too, then a general blue square is shown.[/Background Info]
However, I am pretty confident that these things are not required to be manually specified by a developer.There should be appropriate calls available somewhere.You really should ask D-Iivil since he has extensive knowledge and experience in theme making.
In any case I do not believe this is too big a issue to be worked on at expense of other areas, and I would consider it a bonus if you were to devote any time resolving this.I love your app and probably you should invest your time in improving other areas (or more requested features) first