I solved it by using it in a separate Require() function instead of loading it at the top with dojo libraries.
require(["https://cdn.datatables.net/v/dt/jq-3.2.1/dt-1.10.16/datatables.js"], function () {
$(document).ready(function () {
var table = $('#customerTable').DataTable();
});
});
Surprisingly despite of this new require function itself being inside the main require function, where the dojo is loaded, this works somehow.
require(["esri/Map",
"esri/views/MapView",
"esri/layers/MapImageLayer",
"esri/geometry/Point",
"esri/geometry/projection",
"esri/geometry/SpatialReference",
"esri/symbols/SimpleMarkerSymbol",
"esri/symbols/SimpleLineSymbol",
"esri/Graphic",
"esri/layers/GraphicsLayer",
"dojo/domReady!"],
function (Map,
MapView,
MapImageLayer,
Point,
projection,
SpatialReference,
SimpleMarkerSymbol,
SimpleLineSymbol,
Graphic,
GraphicsLayer) { ... //New Require Function