data.inst.get_path().length
1 はルート ノードです。
.bind("select_node.jstree",function(e,data) {
      var inst=data.inst;
      var level=inst.get_path().length;
      var selected=inst.get_selected();
      var id=selected.attr('id');
      var name=selected.prop('tagName');
      console.log(name,id,level);
  });
(dom で検索する代わりに、inst を使用することをお勧めします);
$(function () {
	$("#demo1").jstree({ 
		"plugins" : [ "themes", "html_data", "ui", "cookies" ]
	});
	$("#demo2").jstree({ 
		"plugins" : [ "themes", "html_data", "ui", "cookies" ]
	});
  $('#demo1,#demo2').bind("select_node.jstree",function(e,data) {
      var inst=data.inst;
      var level=inst.get_path().length;
      var selected=inst.get_selected();
      var id=selected.attr('id');
      var name=selected.prop('tagName');
      console.log(name,id,level);
  });
    
});
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/jstree/3.2.1/themes/default/style.min.css" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/1.12.1/jquery.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/jstree/3.2.1/jstree.min.js"></script>
  With id-s:
<div id="demo1" class="demo">
	<ul>
		<li id="phtml_1">
			<a href="#">Root node 1</a>
			<ul>
				<li id="phtml_2">
					<a href="#">Child node 1</a>
				</li>
				<li id="phtml_3">
					<a href="#">Child node 2</a>
				</li>
			</ul>
		</li>
		<li id="phtml_4">
			<a href="#">Root node 2</a>
		</li>
	</ul>
</div>
  Without id-s:
<div id="demo2" class="demo">
	<ul>
		<li>
			<a href="#">Root node 1</a>
			<ul>
				<li>
					<a href="#">Child node 1</a>                   
				</li>
				<li>
					<a href="#">Child node 2</a>
				</li>
			</ul>
		</li>
		<li>
			<a href="#">Root node 2</a>
		</li>
	</ul>
</div>