I love 40 breeders and use them for both snakes and Leos. I agree with the previous response that finding a way to seal the top of the divider would be a challenge. Is it a critter cage with sliding screen top? If it's an actual tank with separate lid it would be easier to divide. I divided my 55 gallon tanks when I had baby beardies. I attached some of that tank backer to the divider so they could not see each other, you might want to consider attaching something to block their sight. Not sure if seeing each other would or would not cause stress.
You can do a really nice setup in a 40, I think it's a nice sized tank for one adult. I say go ahead and spoil your snakes and buy a second tank and give each his own, then you won't have to worry about having to buy a new tank down the road when they grow up!
This is my Rat Snake's 40 Breeder...

Here is Mysty's 40 Breeder, I still need to get her some plants to spruce it up a bit...

I also house my Sand Boa in a 40 Breeder, he's less than 2 feet long but very active and makes good use of the extra space.
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Lyns Lair
Frogwatch USA
WNY Herpetological Society
0.1 Cat (Mia)
4.2 Ferrets (Wolf, Shadow, Verdell, Sullivan, Boo, Peach)
1.0 Carpet Python (Bear)
1.0 Malagasy Blonde Hognose Snake (Wilbur)
1.0 Yellow / Everglades Rat Snake (Pumpkin)
1.0 Russian Sand Boa (Fang)
0.1 Normal Corn Snake (Mysty)
1.0 Banded Water Snake (Ripley) coming soon!
1.0 Whites Tree Frog (Trevor)
2.0 Solomon Island Eyelash Frogs (Chompy & Grimli)
1.0 AFT Gecko (Cocoa)
5.6 Leopard Geckos (Trouble, Scooter, Simba, Firenze, Teddy, Nala, Mystique, Freckles, Dotty, Zipper, Twister)