I doubt it is related to 1.08 or 1.09 seems a hardcoded bug present from start.
I further tested the issue and managed to determine the causes.
If a nation is not part of axis, allies or comintern AND is not allied with any other country THEN it is unable to perform Shore bombardment missions on his own territory [the option from all context menus simply disappear]. Thus the bug does not affect UK, GER and SOV at all [as they are all in "named" alliances]. However USA, JAP and every other country not in any type of alliance is plagued by it.
The example presented above is right, jap without any allies [after booting MAN] cant shore bombard. but an even better example is USA which is unable to perform that mission 36jan1.
I confirm this as a bug, because it makes no sense UK and GER can shore bomb own shores while USA can't and not because techs or doctrines but simply because of being in an alliance or a named alliance.