Boni dislikes being moved from his spot. So, why does Berk insist on bringing him out, such as when they go fishing or for their picnic? Of course - because Boni is always complaining about being bored!
Why Berk doesn't just cement the Trap Door shut - it's where most of his ingredients come from! (Not to mention all those lovely worms Drutt likes.)
Berk did try nailing it shut in "The Thingy", which lasted all of five seconds when something really big burst out. Presumably, he doesn't bother anymore because of this.
'Im Upstairs may be an Eldritch Abomination, but he is civilized and living under his roof offers Berk and his friends safety from the barbaric monsters that live down the Trap Door (and probably around the castle as well). See how all the monsters retreat once the Thing Upstairs yells at Berk. Plus, if you consider the games canon, he even pays Berk for his work.