I have map with two layers (shapes and bubbles).
Seems i can use tooltips only on active layer
There is a bug in the Kendo Map widget where only the last layer raises the shapeMouseEnter, and if I recall correctly, your map uses this event to create and show tooltips.
You can track the progress of this issue in the following page: https://github.com/telerik/kendo-ui-core/issues/2473. I have also raised its priority.