I'd have to guess that this is by design. The Replace command is too dangerous.
Not a solution (sorry), just an observation.
The replace can be scripted and the dialog supressed. That may do what you need.
As David suggests, Replace requires a specific User click. Apple Interface Guidelines suggests that the least-dangerous button always be the default in scripting. And that default may be activated via hitting return (which in this case is the Cancel). It makes perfect sense when you think about it.
In addition to suppressing the dialog if scripted, you can first provide the User with Custom Dialog message and only proceed if click OK (which you CAN make the default thus activating upon hitting Enter).
Thanks for the answers.
This is not for the enduser, but for me when I'm editing current information. I can't count how many times I have done a Replace during the years as a developer...
Of course there is no obvious shortcut because it's quite a dangerous thing to assign a shortcut to. However, there are many equally dangerous shortcuts in Mac OS. Eg, COM+D for "Don't Save", COM+Backspace for the same task in Mountain Lion, In FM add Alt to COM+E and you don't have the "Do you really want to delete this record" dialogue, etc etc.
In the end, it's up to me as the user/developer if I want to risk to learn those "dangerous" shortcuts.
Sure.. But FMI is not going to provide it too you because they are mor interested in making fM idiot proof for beginners. Their choice and you are not going to change their minds -:)