Is there a way to change the purchase currency to scrap? Also is there anyway to remove the item like not for sell or even show up on the list? I know i can remove the catogories. But some item are still in certain catogories i cant just disable the whole thing.

You are free to remove everything in the item list in each of the shops.
But not the items themselves inside the config.

( they auto regen at the bottom of the config if you attempt to remove the items)

Correct Example; 

    "Fun": {
      "DisplayName": "Fun",
      "DisplayNameColor": null,
      "Description": "You currently have {0} coins to spend in the Fun shop",
      "DescriptionColor": null,
      "Permission": "",
      "Currency": "",
      "CustomCurrencyNames": "",
      "CustomCurrencyIDs": 0,
      "CustomCurrencySkinIDs": 0,
      "EnabledCategory": true,
      "EnableNPC": false,
      "NpcIds": [],
      "Items": [
        "Blue Boomer",
      ]
    },

As far as Disabling a whole shop category goes you simply toggle EnabledCategory to false if you don't want it.

    "Fun": {
      "DisplayName": "Fun",
      "DisplayNameColor": null,
      "Description": "You currently have {0} coins to spend in the Fun shop",
      "DescriptionColor": null,
      "Permission": "",
      "Currency": "",
      "CustomCurrencyNames": "",
      "CustomCurrencyIDs": 0,
      "CustomCurrencySkinIDs": 0,
      "EnabledCategory": false,  < Set to false
      "EnableNPC": false,
      "NpcIds": [],
      "Items": [
        "Blue Boomer",
      ]
    },