Yes, super shotgun hits everyone multiple times.
You don't get it from Mary's Blacksmith, you need to go to town hall and build the upgrade hut if you haven't already (for two basic gemstones), then you need to, again in the town hall, go to "upgrade", then "building upgrades", and buy "Upgrade Hut Mythical Weapons" for 1 diamond from the mines, and 300 gold. Then go to the Upgrade Hut when you have it unlocked, and you'll be able to craft mythical weapons there.
Cecille and the others DO return at some point, but honestly, the biggest thing you should've made sure to get was Lyra's blessing before moving on, but I can't remember if that was an event where you had to go to her in the tavern for, or if it was just a side quest in the capital city.
Which I believe all side quests are technically playable in any order? I'm not sure as I always played them all in order myself, but the notifications about the tavern are primarily about Juggernaut, as you have the chance to challenge her as long as she's in the tavern, but beyond a certain point, she won't be anymore, that's legitimately up to you though, since Juggernaut is one of the hardest optional bosses in the entire game. If you just want a casual playthrough, you don't have to beat her.