I can't think of any reason why knockback would have been affected, shotguns or otherwise. Almost none of the enemy stats were changed, nor were there any stat changes to shotgun missiles or weapons. In fact, having played through two games and built a tactical shotgun in both of them, I found it to be one of the more reliable weapons I used BECAUSE of the knockback.
A lot of so-called difficulties could very well stem from the fact that everything (the player as well as all enemies) took a one-tile vision hit. Mostly this has to do with the graphical version, but at the same time I think reducing the sight radius will encourage more off-screen tactics, which are really important when it comes to the more deadly enemies and higher levels of play. However, if anything, shotgun knockback should appear slightly better, since your in-vision shots have to be closer than before.