a.js

const targetData = [0,[1,[2,[3,[4,5,5],[4,5,5]],3],[2,[3,[4,5,5],[4,5,5]],[3,4,[4,5,5]]]],[1,[2,[3,[4,5,5],[4,5,5]],3],[2,[3,[4,5,5],[4,5,5]],3]]];

function setKey(o, key) {
    const obj = Object.assign({}, o)
    const str = JSON.stringify(key);
    if (str in obj) {
	obj[str] += 1;
    } else {
	obj[str] = 1;
    }
    return obj;
}

function f (data) {
    var inner = function(data, result) {
	var r = setKey(result, data);
	data
	    .filter(function(e, i, a) {
		return Array.isArray(e)
	    })
	    .forEach(function(c, i,a){
		r = inner(c,r);
	    });
	return r;
    }
    return inner(data, {});
}

console.info(f(targetData));