If the slide was empty (blank) then your code would error as Shape(1) does not exist.

If you have On Error Resume Next somewhere in the code then it would just go to the next line and increment the counter

Sub countme()
Dim j As Long
Dim nbrTitre As Integer
Dim Pres As Presentation
Set Pres = ActivePresentation
nbrTitre = 0

For j = 3 To Pres.Slides.Count
If Pres.Slides(j).Shapes.Count > 0 Then
If ((Pres.Slides(j).Shapes(1).Width = 648) And (Pres.Slides(j).Shapes(1).Height = 90)) Then
nbrTitre = nbrTitre + 1
End If
End If
Next j
MsgBox nbrTitre
End Sub
If you are trying to check whether the slide has a Title Placeholder you can do this with

if Pres.Slides(j).Shapes.HasTitle