Ok, after doing a bit of digging into MSDN, I believe I have found a way to find this out. In the T4 template I can access properties as follows:
if (navProperty.FromEndMember.RelationshipMultiplicity == RelationshipMultiplicity.Many &&
navProperty.ToEndMember.RelationshipMultiplicity == RelationshipMultiplicity.Many)
{
// deal with many to many link collections here...
}
Posting it here in case anyone else has a need for this.