Do level 2 and 3 allies count seperately towards the 45 total?
I don't believe they do. I think you need 45 unique allies. Which isn't too hard. If you look at my page (here), you'll see I've got 43. I've got zero A-Rank allies (Z-Dog, Big Bo, Big Sham, Big Ro) and zero trade allies (Hyuk, Right, Anonymous, LisaLisa), I don't have any season 2 allies (Cato, Doughman), I don't have the new ally (the one related to hanging out with people, that no one has yet), and I don't have the HoClause. Also, I'm not WhiteEye, so no Ol' Whitey. So, by my count that means there's 56 potential allies in season 2. 54 if you're in season 1. 53 if you missed the HoClause. 52 if you're not WhiteEye. That's still plenty to hit 45 before you loop.
Ho-Clause doubles Ally Drop rate and Chance of finding allies.
I am Gokol and HInata on BvS.
Back has one jutsu called Ninjamas Spirit
It doubles friendship earned on a mission.
I forget what it costs.
The HoClaus doesn't increase the chance of finding allies. =x
EDIT:
The HoClaus
Ally Drops appear 50% more than usual!
From The HoClaus:
The Ninja-Mas Spirit
XP: 100000
Double Friend Points given
20 C
Since it is not possible to get Themes during the first Season (there's only 1 exception afaik), will I get the
"All Together Now"-Theme after looping if I have got 46 allies in Season 1?
Or is it rather senseless trying to get 46 allies during Season 1?