Microsoft pushed out version 22.214.171.124 of the AAD Connect synchronization utility earlier this month. Unfortunately, the new software removes disabled on-premises user accounts from Azure AD, which means that on-premises shared mailboxes disappear for cloud users. Microsoft has released version 126.96.36.199 but maybe it’s better to go back to a version that you know works. At least until after the holidays.
Disabled accounts are synchronized as well to Azure AD. Disabled accounts are common to represent resources in Exchange, for example conference rooms. The exception is users with a linked mailbox; as previously mentioned, these will never provision an account to Azure AD.