I’m sure that’s very frustrating. I’m not sure where you heard that smartthings is “the best“ but every system has pluses and minuses. The biggest plus for SmartThings is the ability to upload your own custom device type handlers and the ability to support very complex rules logic. The biggest minus is reliability and the fact that things change all the time, making troubleshooting challenging.
I personally would never use SmartThings for third-party installation: I think the maintenance costs would eat up all my profits. But obviously that’s a personal choice.
Even for my own personal use, I expect an MFOP ( maintenance free operating period) of at least six months and preferably a year. I do get that from a number of home automation systems, including the Phillips hue bridge, Logitech Harmony, apple’s HomeKit, wink, Amazon Echo, and Lutron Caseta. But since November 2015, I have yet to get an MFOP from SmartThings of longer than two weeks, and usually it’s closer to 10 days. 
So I personally have moved all of my critical use cases over to other systems. I still use SmartThings for complex convenience cases, like getting a notification that the guestroom window is open when rain is expected and the guest is away from the house, because it does that much better than anything else in that price range. But the reliability just isn’t there for me on something like turning The entry light on every day at sunset. 
The zwave repair utility
As far as zwave repair, you are right, it is ridiculous that support tells people not to run it. Most of smartthings’ zwave competitors have running a weekly repair as part of normal maintenance, which is what the standard expects. But they’ve been saying that for about two years, so I can only assume that it has something to do with their cloud platform and things getting out of sync that way.
This week specifically
Some people have also been reporting some specific problems of the type you’re describing this week, apparently due to problems with the recent hub update. See the following thread (this is a clickable link)
Going forward
I wish I had better advice for you. I know you are already working with support. But at least I can confirm that the problems that you are seeing do come up for some people with SmartThings. Not everyone all the time, but definitely more than with a number of other platforms.
http://thingsthataresmart.wiki/index.php?title=Bug:_First_Reports
The only good news I can give you is that it looks like most of the individual devices that you have selected are of high quality and the problem is not zwave itself. (The Monoprice and Ecolink Devices are budget brands, and not quite the same quality as your other devices.)
One Pro tip
As a former field tech (I was a network engineer before I ever bought SmartThings for my own use), The only specific advice I would give you is that if you are saying you are adding more than 25 devices on one day, then, yes, that’s probably going to crater the network. It takes time for address table changes to propagate. I would not add more than two dozen in a 48 hour Period.
If you are going to do a big installation at a customer’s house, then Most professional installers would do bench pairing back at the warehouse and get all the devices added to the network over a week or two before you ever go out to the customer’s Location, giving the hub plenty of time to update all the routing calculations. Then after you install in place, run a zwave repair. Make sure the customer understands it may still be a day or so until the network is running at maximum efficiency.
Also, it may help to know that smartthings staff has said repeatedly that their typical customer has fewer than 15 devices and never uses any custom code of any kind, including webcore. So that’s their sweet spot as far as both network efficiency and customer support are concerned. People here in the forum will be happy to help troubleshoot if they can, but there’s only so much we can do.
Counter examples
And I should also say that there are some people in this community who have a couple of hundred devices and have done an entire home (or two) with the Fibaro kit and are very happy with it, although again the hands-on maintenance requirements may be higher in terms of time then most third-party pro installers would want to work with.
Anyway, take a look at some of @anon36505037 ‘s projects as a good example. He may have some additional ideas As well.
https://community.smartthings.com/t/new-house-build-update-uk/131433/