I have built many apps both desktop (i.e. client-server type) and now tons more web-based apps. Deploying changes is MUCH easier with a web app than desktop. That is an important consideration. I am not sure how many users for your app. If it is only in a single office, then you can always remote into the server for your updates. But if people are installing from all over the place, then you will have to "push" your changes to their various servers or provide a way that they can update themselves. With all the different computers, configurations, network issues, etc. you may get various questions if something "doesn't work" or doesn't install correctly. For a web application, I just have to make sure it supports the various browsers and I can deploy my changes easily. The web application can also ensure security too if you have many users from all over the world. Security is also the other important consideration. If you do things right, you should be ok there too.
Hope this helps