Only people on the land/sea package can check in at their WDW hotel for the cruise....others that are on the bus but just had a room only ressie will still have to check in at the port.
There may not be long lines to check in when buses arrive from WDW (because they ususally come after boarding the ship begins) but there will be very long lines for boarding if they have not let the folks onboard yet....so arrive earlier. Buses do come earlier from the airport and those people will be checking in and can cause long lines.
Hope that was not too confusing!!!
MJ