If it is a joint checking account than the refund check can be deposited into the joint account with only your husband endorsing the check.
You both do not have to endorse the check.
Are you sure that a government issued check (eg. these checks were from the IRS) to a husband and wife (they use different last names) can be accepted for deposit into a joint account by only one of the two parties named on the checks. What prevents one of the two people, in this case the husband from stealing the money as he did, by transferring the money out of the joint account into his own individual account the next day?
Normally financial institutions accept the IRS refund check if it is written out in joint name and deposited in joint account. If you were to cash the check than you would need the signature of both the parties named on the check.