The answer was given in the tycho mailing list some time ago:
http://dev.eclipse.org/mhonarc/lists/tycho-user/msg01001.html
The details:
OSGi does not have a notion of "snapshot" versions, all versions are treated the same and 1.0.0.qualifier is indeed considered to be newer than 1.0.0.
There are two versioning schemes that result is reasonable behaviour both for OSGi and Maven.
Use the same four part version (eg., 1.0.0.20111112-0735) for both Maven and OSGi. This results in slightly odd version jump when going from snapshots to releases on the maven side, i.e. 1.0.0-SNAPSHOT goes to 1.0.0.20111112-0735, but everything works otherwise.
Use even/odd convention to version snapshots and releases, i.e. 1.0.1-SNAPSHOT/1.0.1.qualifier is released as 1.0.2/1.0.2.
I think it is also possible to decouple maven and osgi versions of released artifacts, i.e. use 1.0.0 for maven and 1.0.0.20111112-0735 for OSGi, but personally I find this confusing and would not recommend. And I am not sure if Tycho will allow this in the future.
-- Regards, Igor