The long story short is it worked for me as expected out of the box! :smileywink:
Okay, here is what I did...
In VMware Fusion > Preferences... > Default Applications, I have the "Open Web Pages (http, https) with: Safari" check box checked.
In the Windows 7 x64 Virtual Machine > Settings > Default Applications, I have the "Open your Windows files and web links using Mac applications" check box checked.
I downloaded the "NOTES_9.0_WIN_EN_EVALUATION.exe" file from ibm.com and installed it in a Windows 7 x64 Virtual Machine under VMware Fusion 5.0.3 under OS X Mountain Lion 10.8.3.
In Notes 9.0 I setup my Email Account as I was installing it and then in Notes 9.0 under File > Preferences...Web Browser, I have the radio button for "When clicking on a hyperlink in the client" set to "Use the browser I have set as the default for this operating system".
Next I downloaded my Email in Notes 9.0 and clicked on a hyperlink and it opened as expected in the Host OS in Safari. I also went back to VMware Fusion > Preferences... > Default Applications and changed the "Open Web Pages (http, https) with:" check box selection to Firefox and then clicked a hyperlink in Notes 9.0 in the Windows 7 x64 Virtual Machine and it too opened as expected in the Host OS in Firefox.
Also make sure In Windows 7 Control Panel that under the Internet Properties Programs Tab that it says "Internet Explorer is not currently the default web browser" and then under "Internet programs" on the same Tab click the "Set programs" button. Then scroll down to the bottom of the Default Programs > Set Associations window and make sure that HTTP and HTTPS are set to "Open URL in VMware Host" and "Default Host Application" as shown in the image below.
(Click image to enlarge.)