Currently, in order to have IBM Companion looking up to the Domino server directory, it is necessary to perform the workaround below:
1. Compose new email in IBM Companion;
2. Select "+" button;
3. Select Groups;
4. Select your IBM Lotus Notes Traveler account (this need to be checked).
This additional step should not be necessary...the default behavior should be perform the lookup at the Domino Directory instead of the local contacts from the iOS devices.