you should better place the UserControl inside a Placeholder
control. Then simply hide/show the Placeholder depending on your conditions.
The Placeholder does not render any tags for itself, so there is NO overhead of outer HTML tags.
I Assume you must have registered your UserControl in your Master page. So, place the userControl now inside a PlaceHolder control.
<asp:ContentPlaceHolder ID="MainContent" runat="server"><!-- Of Master Page -->
<asp:PlaceHolder ID="place1" runat="server">
<uc1:Test ID="Test1" runat="server" /><!-- Our User Control-->
</asp:PlaceHolder>
</asp:ContentPlaceHolder>
and in Code behind::
protected void Page_Load(object sender, EventArgs e)
{
if( _Some_Condition_)
place1.Visible = true;
else
// Hide PlaceHolder and thus all controls inside it
place1.Visible = false;
}