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Why does Wireshark producse such a json structure?

Because it has a routine that puts "plain text" items into the protocol tree, with no field name associated with them, and because it has a JSON printer that, for those items, just prints out the text.

Can't it be fixed?

It can, but it would involve a change such as requiring that routine to specify a named field, so it'd show up as something such as

"lldp.chassis": {
    "lldp.tlv.type": "1",
    "lldp.tlv.len": "7",
    "lldp.chassis.subtype": "4",
    "lldp.chassis.id.mac": "00:0a:25:3a:6c:ee"
},

"lldp.port": {
    "lldp.tlv.type": "2",
    "lldp.tlv.len": "7",
    "lldp.port.subtype": "3",
    "lldp.port.id.mac": "00:0a:25:3a:6c:f1"
}

Please file a bug report on the Wireshark Bugzilla.