First, check out my blog here:

mindsharpblogs.com/.../1680.aspx

I don't know a way to bulk check-in. In fact, it was coded that way
(from my conversations with MS) so that users were forced to enter
metadata.

Can WebDav and all other multiple-upload vectors be disabled?

You can disable Webdav, either from IIS (not recommended), or through
the Web Application Policy on the relevant zone.

For example, from Central Admin, Application Security, Policy for Web
application, you can modify the policy for all zones, or create the zone
from where you want to restrict Webdav access. From 'Policy for Web
Application', notice that (all zones) is the default scope for
policies. You will notice the local service (used for IIS caching) and
the crawling accounts. Don't modify these. You can select 'manage
permissions policy levels' from the quick launch on the left-hand side,
and create (add) a custom policy that will deny the "Use Remote
Interfaces - Use SOAP, Web DAV, or SharePoint Designer interfaces to
access the Web site" permission level from a user or group (like
domain\authenticated users). These Application Security Policies
OVERRIDE all site collection policies, fwiw.

Test this before implementing in production. This is not simple and you
can hose your installation quickly without a proper understanding of the
impact

This is indeed the way it works. Worse yet, until CheckedIn the first time
only the author will be able to see the documents  (not even an Administrator
will see them) and they still count against the disk quota for the site.

Also, I know of no way to checkin multiple  documents at a time. It could be
done with custom programming so it may exist in a 3rd party product, but
there is no way in the OOB interface.

To check -in multiple  documents - in SP2007:

Go to the site or library where your documents  reside.

Go to:
Site Actions> View Reports > Checked Out To Me
(Assuming you have proper credentials on the site)

Next:

Select the library or folder from the available tree. In the top
tool bar of that window you will see a link that either reads "Show
Related Resources" or "Hide Related Resources". Cliking on that link
area will toggle between the two.

Select "Show Related Resources".

A window should open with your documents/pages/files and a square
checkbox preceeding each item in the left column.

You can check the files individually or if you click the multiple
icon box at the top it will select all.

Go to:

Actions > Check In

A comments box will appear which you can leave blank or comment. Of
course your comment will apply to all documents selected.

Close the window and your documents are all checked-in.

But, it only seems to work in Publishing sites

I was able to append the URL to a WSS V3 site collection, but it didn't
return the desired results. I bet there is a way to do this?

Most of my sites are Team Sites and I've checked in thousands of
files using this method. Again, I'm working in SP2007 and not 2003.

On occasion, I will have issues but if you poke around enough you
will find the solution. I stumbled on this bulk check-in by "poking
around" AFTER I had to check in a few hundred files individually.

Tedium breeds knowledge and skill.