Serialization may be affected. If you have classes that need to be
serialized, the engine includes type information in the serialized data,
that way it can be reconstituted later. If you the AssemblyFormat property
is not set correctly, you could end up with a situation here you have stored
some data, upgraded your application (maybe because of a bug fix), and then
error when you try to load your serialized database (even though nothing in
that particular class has changed).
I would say maintenance is a big drawback. Unless your assemblies need to
be placed in the GAC, or run as COM+ component, or some other special case,
strong-naming them probably is not necessary.