So you are actually going Schengen to Israel, and as for your original question, Israel would never let you board a flight without going through security at ATH...
As KLouis said, luggage would be checked from NRT to ATH, you would do immigration in WAW, and at ATH you have no option other than to go landside.
The flight to TLV will probably have additional security and 4 hours is still probably OK. If it were another non-Schengen destination 2.5-3 hours might be enough for a self-connection.