Welcome Cadetspangler. There is footage of him doing this I believe somewhere, it's done by trained professionals, bees don't sting much, because after they do, they die. I'm sure it's very scary but he won't have been stung much if at all. I'm sure I watched/read something re this, but don't recall where.
Yes, as you probably know far better that I do, many sticky situations on Malcolm are left up the air, so we never got to know how they recovered from all those injuries you mentioned or how they got rescued or off the hook.
That's due to the episodic and comic nature of the show I guess, where a lot of things aren't developed from one chapter to the next logically.
Sometimes I think this is a pity, but I've recently been watching one comedy which spent a number of episodes developing one particular situation all lead characters got stuck in, and this really got tedious, even though the acting was fine and there were many well-written lines.