The ball passes onto Shedinja in any 3rd gen game. Even if it didn't, there's nothing stopping you from trading to the game that does work.
Also, you neglected to take encounter slots into account. And for what it's worth, def/spdef matters when a Substitute is passed.
Edit:
I never investigated wild captures on R/S box, sorry. The lack of Sync for natures makes it very unlikely that what you want is possible.
Oh sorry my bad, I forgot to check the encounter slots :/ I will edit the post when I'll finish to check. Thanks for your reply Hozu.
EDIT:
Adamant 00 / 31 / 00 / 00 / 31 / 31 = It isn't possible;
Adamant 00 / 31 / 31 / 31 / 31 / 31 = Possible (
Method 2);
Synch Encounter Slots: 0, 1, 2, 3, 4, 6, 8, 9
W/O Synch Encounter Slots: 2, 10
Lonely 00 / 31 / 00 / 00 / 31 / 31 = Possible (
Method 4). I assume that Nincada is always generated by Method 2 in Emerald. I know that some Pokémon are generated via Method 1 & 4 in RS / FRLF but I don't think that Nincada could be generated by Method 4.
Synch Encounter Slots: 0, 1, 2, 3, 4, 5, 7, 9
W/O Synch Encounter Slots: 1
Lonely 00 / 31 / 31 / 00 / 31 / 31 = Possible (
Method 2);
Synch Encounter Slots: 0, 1, 2, 3, 5, 6, 8
W/O Synch Encounter Slots: 0
Lonely 00 / 31 / 00 / 31 / 31 / 31 = Possible (
Method 2);
Synch Encounter Slots: 1, 2, 3, 5, 6
W/O Synch Encounter Slots: 1
Lonely 00 / 31 / 31 / 31 / 31 / 31 = Possible (
Method 4).
Synch Encounter Slots: 0, 1, 2, 3, 4, 5, 6, 9
W/O Synch Encounter Slots: 4, 6
The last spread is Method 4, in the previous message I wrote Method 2 instead of Method 4. Sorry about that.