Whatever permissions you deny, will cause facebook to stop sending that information. For example, if you deny the user_checkins permission, then facebook will not tell the app about any checkins you have. If every third post in your statuses is a checkin, they simply won't be returned in a query. In general, denying the user_* permissions just makes that type of object not be returned in a query.

The pubish_* permissions are, as expected, the ability of the app to publish that type of object on your behalf. If you deny the publish_checkins permission and never try to do a checkin, you will not notice the difference. If you do try to publish a checkin without the permission, you should get an error that (I think) the app will show to you. (I am only slightly uncertain because I do check the returned info for these types of errors, but facebook doesn't really give great error messages for everything.)

In any case, you can deny the permission for either reading or writing checkins and the app will work fine. Feel free to try it...you are certainly thinking of things that I didn't consider, you won't break anything by trying, and I (and I'm sure others here) will appreciate hearing the results of your testing.

Also: if you are interested in seeing what the backend does with your permissions, you can check out the source code at Gitorious. It is always stressful to cede permissions on facebook because you don't know what will be done with your data. But the great thing about open source (and platforms like Maemo that encourage it) is that even if you can't read the source code yourself you can be reasonably assured that someone else would spot nefarious code.