Welcome, and good job separating them from time to time! I think you are doing a great job!
The shelter on the other hand... in my opinion, no reputable shelter would adopt out two healthy puppies that could otherwise go to two separate home. No less, insist that an adopter get two especially when you originally wanted one. Unfortunately, littermate syndrome is not something a foster parent, shelter, OR vet would see (plus, vets are usually not behaviorists or trainers so sometimes their behavior advice can be lacking) with young puppies. It doesn't spontaneously happen with very young puppies. This is why the socialization period and early stages in life is the window people have to prevent it. It is the attachment littermates (or any young, impressionable dogs) form over time to the point where it becomes a dependency. It is when they choose each other as comfort in a questionable situation rather than learning to cope or depend on the owner. It is when the puppies affect each others personality (one is usually a little more brave, pushy, domineering, etc. and the other is usually a little more laid-back, fearful, etc.). Or worse, if both pups are fearful.
Here is a good article:
https://blog.betternaturedogtraining.com/2013/07/18/littermate-syndrome/
Key point is, they need to spend SIGNIFICANT amounts of time away from each other, in a positive way. I know someone experienced in training and breeding who owns a boarding facility. She purchased two littermates. And she is literally taking one puppy to my puppy class one night of the week, and the other puppy to the other puppy class another night of the week. I hope she is doing more than just that, but it's a good start.
So, I'm not trying to fear monger or anything like that. No one is saying your pups WILL develop this, but it is a real risk. And like I said, I'm glad you are loving your pups and helping them grow to be their own individual dogs!