As far as I can tell, only some of Verizon's pre-installed apps for the D3 require this to be installed - the Family Locator service app, VZ Navigator, and maybe City ID.
My guess? Just based on its name, Verizon uses an SMS "message" to have the phone wake up and locate itself, and this app manages the communication between text messaging and those VZW apps (as well as preventing the normal SMS app from seeing the SMS messages - in other words, it intercepts those special messages before the text messaging app even sees them.)
It's just a guess, but I found that app listed in the required permission on the AppBrain market. See here:
VZW Family Locator | AppBrain Android Market (go to the "Permissions" tab".)
Minimoto does not include that vzwappdirectedsmspermission.apk file, but when I saw the "SMS" in the name of the file, I decided that it may be necessary for Blur messaging. After installing the patch, I did a little research to discover that it does not appear to be used. Plus, of course, I can send and receive text messages without that .apk file being present.
When/if the next Minimoto version comes out, I'll test my patch again, but you may want to go up to my message where I uploaded the patch and download the new one - I updated it last night. It's here:
Post 146.