This is the way it is designed to behave. When you compare a string with another value for equality it converts the value to string. The other option which is to implicitly convert the string to a number will throw an exception if the string is not a number.
You will need to explicitly convert the string to number:
Code:
Dim s As String
s = "0.00"
Dim n As Number
n = s 'explicitly convert the string to number
If n = 0 Then Msgbox(True)