I will answer your question based on my experience. I cannot speak for everyone in this forum. So I hope they go easy on me.
Answer to First Question:
Speed: Yes, there's a huge difference in speed. If you don't have an fast asymmetrical internet connection, you can forget about using WebDirect. This whole week has been a nightmare for our company. We have lost so many orders due to clients unable to place their order online. Every single letter they type, the database has to refresh to a point where it's completely unusable.
Kicker: And I'm only talking about the clients that were able to log in, who knows how many were not able to log in because the database kicks them out if they are not using a compatible web browsers and you "the developer" won't even know about it. The clients only see a message that says "The web browser you are using is too old or not supported. Please use a supported web browser." and that's it. Leaving the clients stuck with a page with one line with no information as to what are the supported browsers, etc.
SSL: There's a thread about installing SSL here in the forum. The security of FileMaker is great, but getting it to install is ridiculous because it requires you to use command line and fiddle with the actual serverCustom.pem to make it work. With the help of some users like Mac89, we were able figure out a work around. But still, you would still need to redo the work around every time you restart your server because the SSL would stop working.
Mac Server: If you have a Mac Server and uses the Server.app for your web services, you can forget about it. In fact, I had to uninstall the whole Server.app just to make it work without incompatibility issues. Which means I lose FileSharing, Users, Messages.. you know all the cool stuff that makes the Mac Server awesome.
This weekend, I would be downgrading to FileMaker Server 12 (I'm not even sure if it's backwards compatible). It's just so frustrating and it's hurting our business. At this point the shortcomings of FMS13 clearly outweighs it's awesome features.
Answer to Second Question:
I don't think you can use IWP and WebDirect at the same time on the same machine. If you upgrade to FMS13, then both Database A & B will be using WebDirect. Unless you have 2 machines with 2 different versions of FMS.
I want to wish you good luck on installing FMS13, but luck is not enough, what you need is for FileMaker Team to make a serious update.
I haven't had quite the experience you have reported, but my environment might be different than yours.
I have already installed FMS 13 and have been running it for a few days now.
I manage multiple servers for different functions, so I don't have the need to run other OS X Server services on the same hardware as FMS. If you can afford multiple hardware this is highly recommended for several reasons, some of which you have been running into (although I do understand that option isn't best for everyone).
Regarding IWP and WebDirect on the same machine, I think you can. The setup wizard asks which services you want to enable, and IWP is one of them. Unless that means that the WebDirect feature isn't working, but that isn't clear.
Anyways, I would still be interested in hearing if there are significant perforce differences between IWP and DirectWeb, and clarification on how you can determine which technology is being used to serve up the solution...
With all due respect sir Joel Anderson, I didn't find any option to enable IWP on FMS13. And on the FMS13 deprecated features list, IWP is the only one feature that were removed from FMS 13.
How I wish we were able to buy multiple servers like you, but we can't so there you go.
With our current internet setup, which is a pathetic T-1 line, WebDirect is unusable. When we get our 20mbps Fiber line next month, I'll be able to compare IWP and WebDirect better and report it back here.
How did you install your SSL by the way?
Looks like you are right, I don't see IWP in FMS13 — I could have sworn that was one of the check boxes, but I must have "read" in my mind Instant Web Publishing, when checking the "Web Publishing" box.
I used the command line tool, which is pretty typical. I manage 20+ servers with various services and they all use a command line tool and involve jumping through hoops for the registration process, so I didn't see the FMS SSL process any different from the other serves I have installed SSL certs on.
So, did you actually install SSL on FMS13 and didn't run into problems?