That shouldn't be happening e.g. the items should receive a hover class, even if they are template items.
For instance the server side templates demo -- http://demos.telerik.com/aspnet-ajax/combobox/examples/functionality/templates/defaultcs.aspx
does have templates, much like your case and has hovering.
Which leads me to believe that there might be something in your projects that prevents the items from being hovered, or overrides their looks.
Which version of the controls are you using? I am asking so I could create a simple example with item templates and test locally to see if the problem exists. If can't produce the problem locally, I will send you the example, so you could test in in your environment.
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