I have a slightly different take on this...
Does it matter which of us opt for the childcare vouchers scheme (both employers offer one)?
If there is any chance of you having another child it might make a big difference, but it gets complicated. If your employer would normally pay SMP only for any part of your ML, you might want to take vouchers yourself as due to an unintended consequence of current legislation, most employers continue to provide childcare vouchers during ML and they are not allowed to deduct the sum from SMP. But beware that if they only pay SMP during the first 6 weeks of ML (ie 90% of earnings during the qualifying period) this has an adverse effect - I said it was complicated!
Another factor is the ease of using the vouchers - Computershare have a particularly bad reputation for the quality of their systems so if you can steer away from them, do.
Does the scheme have any effect on pension contributions?
It shouldn't do - it is very easy for your employer to make arrangements so that it doesn't, and most employers have done this. Do check with the employer(s) though.
can you 'get back' vouchers if you overpay?
Do you mean if you get more vouchers than you need so you want to return the vouchers and get paid cash instead, or do you mean if you pay more to the after school club than you use in childcare can they give you a refund?
If it is the first, most schemes allow you to withdraw vouchers and be paid the sum through payroll instead as a one-off but this provision is designed to cater for unforseen and possibly tragic circumstances and should not be relied upon generally. Check with your employer how they operate this policy.
If it is the second, then generally no. The vouchers must be used to pay for childcare by a registered provider so once you have used them to pay for that childcare, you can't get a refund.