I hope little Alfie is settling in well; Dachshunds are great fun!
I am surprised the breeder didn't realise that both testicles weren't descended and had told you it was just one, however this may have been a genuine mistake.
Whether he had 1 or 2, the surgery would not cost much different to be honest, as the main cost is the anaesthetic, surgeon's time etc.
It is common for cryptorchid surgery to cost substantially more than regular neutering as it takes longer and is a more complex procedure. If the breeder has no experience of this, they may not have realised.
Not neutering him is not advised as this can result in testicular cancer in later life.
In my experience, it is the owner that tends to foot the bill unless an agreement was made before the purchase of the pup, which would be very rare.
No harm in asking for e.g. the difference in cost between this and a regular neuter but the breeder would not be obliged to pay and it would be a gesture of goodwill on their part