I'm currently playing all the mods 7 version 0.4.30 and I found that harvest pylon would work a while with hoes I gave to it but after a while probably within a hour, it stopped working and whole row of hoes were gone. I don't think it's normal because it has cost me several hoe like tools that I created with silent gear and each has 4k durabilities.

Depending how fast your crops are growing, that's certainly possible. Each crop harvest consumes 1 durability, so that's up to 80 durability every 3 seconds for a 9x9 field at full speed. If you enchant them with unbreaking they will last longer, or you can use an unbreakable hoe like allthemodium or supremium.