I think maybe put ; after the first command before issuing the second
command mkdir

id=`/opt/zimbra/bin/mysql -e 'use zimbra;select id,comment from
mailbox;' | grep $username | cut -f 1` ; mkdir /tmp/$username
2>/dev/null

&/or, possibly you need to escape your statement

id=`/opt/zimbra/bin/mysql -e \'use zimbra;select id,comment from
mailbox;\' | grep $username | cut -f 1` ; mkdir /tmp/$username
2>/dev/null

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