We used SSN + ITIN for married filed jointly last year. This year we used both SSNs. IRS accepted the electronic filing already.
If your spouse with ITIN wants to get economic stimulus payment, better use SSN. Your family would get up to $1200 based on your status and your spouse's income last year. For example, if your spouse used EAD to work and earned more than $3000 last year, and both of you file as 1040(not NR). Your family may eligible to get the maximum stimulus payment (1200). If she does not use SSN this time, she will lose this handsome paycheck on her side.