I agree with Joe, the best approach is not to modify pages but use the existing functionality of DNN.
Since admin doesn't have a simple check boxes to add remove messages and notification you can address it at the following way.
First address navigation thus if someone clicks on the icons they will be navigated to the place of your choice
Follow the seteps specified by Joe
Click on the icon and go to edit mode
Remove permissions and in advance settings -> Other Settings /link URL: select redirection to a page on your site
Note: it will remove access and navigation
should you need to go back and find the page settings go to Admin -> Page management -and search for messages
the page will appear under profile
Second hide these icons from site
This can be done by changing style sheet
Open Admin ->Site settings -> Stylesheet Editor
Add the following at the and of your stylesheet
.userNotifications
{
visibility: hidden;
width:1px;
}
.userMessages
{
visibility: hidden;
width:1px;
}