Can I specify a single molecule object with multiple disconnected parts in a Ketcher file?

Yes, you can specify a single molecule object with multiple disconnected parts in a Ketcher file.

Here is a simple example of Ketcher file with a single "molecule" object of a 4-carbon chain. But the bond between the second and third carbon is removed with 2 disconnected remaining parts:

{
    "root": {
        "nodes": [
            { "$ref": "mol0" }
        ]
    },
    "mol0": {
        "type": "molecule",
        "atoms": [
            {
                "label": "C",
                "location": [ 0.59, 0.0, 0 ]
            },
            {
                "label": "C",
                "location": [ 1.46, 0.5, 0 ]
            },
            {
                "label": "C",
                "location": [ 2.33, 0.0, 0 ]
            },
            {
                "label": "C",
                "location": [ 3.19, 0.5, 0 ]
            }
        ],
        "bonds": [
            {
                "type": 1,
                "atoms": [ 0, 1 ]
            },
            {
                "type": 1,
                "atoms": [ 2, 3 ]
            }
        ]
    }
}

You can import the above Ketcher file to the Ketcher editor. But it will be considered as a 2-molecule structure. If you export it as a Ketcher file, you will see 2 "molecule" objects like this:

{
    "root": {
        "nodes": [
            { "$ref": "mol0" },
            { "$ref": "mol1" }
        ]
    },
    "mol0": {
        "type": "molecule",
        "atoms": [
            {
                "label": "C",
                "location": [ 0.59, 0.0, 0 ]
            },
            {
                "label": "C",
                "location": [ 1.46, 0.5, 0 ]
            }
        ],
        "bonds": [
            {
                "type": 1,
                "atoms": [ 0, 1 ]
            }
        ]
    },
    "mol1": {
        "type": "molecule",
        "atoms": [
            {
                "label": "C",
                "location": [ 2.33, 0.0, 0 ]
            },
            {
                "label": "C",
                "location": [ 3.19, 0.5, 0 ]
            }
        ],
        "bonds": [
            {
                "type": 1,
                "atoms": [ 0, 1 ]
            }
        ]
    }
}

⇒ Scaling Issue on Importing Ketcher File

⇐ Ketcher File Structure for Reaction

⇑ Ketcher File Format for Chemical Structures

⇑⇑ Ketcher - Chemical Structure Editor