Regarding Mushnik, I've always thought it was pretty clear that he's using Seymour for all the business that Audrey II is bringing to the shop. Prior to the arrival of Audrey II, Mushnik treats Seymour pretty badly, even if its in a comedic way, and, later, he only seems concerned that Seymour doesn't end up leaving the shop in the midst of his new found success.
Seymour's decision to attack the plant from the inside at the end is a purely emotional decision based on his grief over Audrey II having killed Audrey, his true love. He's not thinking clearly in this moment. The "Death of Audrey" sequence (really a reprise of "Somewhere That's Green") can be devastating for the audience, if it's played correctly. Mushnik and Orin are both very cartoon-y characters, so their deaths tend to land as part of the black comedy going on. Audrey's death, in contrast, is a sudden and real end of a character that the audience has come to love and understand. The audience should be grieving her right along with Seymour. In his grief-stricken outbust, Seymour tries to shoot the plant first, but it seems impervious to any sort of conventional attack, that's where the idea to attack with a machete from the inside comes from...it's Seymour trying something...anything...to kill the plant that killed his love.