you could use DATE_FORMAT() to deal with this issue

SELECT T.field

FROM

OPENQUERY(LINKSERVER, 'SELECT DATE_FORMAT(t.field,''%X-%m-%d %H:%i:%f'') as field FROM table t ' ) AS T

the date '0000-00-00 00:00:00' will be replaced by ==> 00-00-0001 00:00:00