can I connect directly output of Atmel (Atxmega16A4) that is 3.3V system to the input of LCD display (KS0066) that is 5V system? I need only one way data transfer. Or do I have to use pull-ups resistors or for example 74HC04 level shifter/translator.
You should be able to do this. It depends on the input threshold of your LCD.
Do not use a pull up as this will expose the higher voltage to your Atmel. If you use a 74HC04 then you need to power it at 3v3 and it is the same problem. A level converter will remove any doubt, but it should just about work without.