As Far As I Know

Simplest way (AFAIK!)

Run this :

Sub markit()
Dim osld As Slide
Dim oshp As Shape
For Each osld In ActivePresentation.Slides
If osld.SlideShowTransition.Hidden = msoTrue Then
Set oshp = osld.Shapes.AddTextbox(msoTextOrientationHorizontal, 10, 10, 20,
20)
oshp.TextFrame.TextRange = "H"
oshp.Name = "Hidden"
End If
Next osld
End Sub

Which will mark hidden slides with an "H"

and this to remove all the marks

Sub unmarkit()
Dim osld As Slide
Dim oshp As Shape
For Each osld In ActivePresentation.Slides
For Each oshp In osld.Shapes
If oshp.Name = "Hidden" Then oshp.Delete
Next oshp
Next osld
End Sub