It will delete them from the 'shell:appsfolder', (I'm not sure about the 'All apps' Menu, they don't show up there on mine anymore), but they will still be associated with your current MS Account in the Store under 'Account/My apps/All apps'.
(Be careful choosing the ones to delete!)
I disagree, In my case I had a lot of issues with 10049(and some issues with 10041) both upgrade & install, I didn't wait on the slow ring iso, don't know if there will be one. I couldn't do a clean install it or upgrade from windows 7 if I did, it crashed a few minutes after use and keep rebooting. I went through an unorthodox way to do a clean reinstall 10049. It is working but still has some bugs, command prompt issue, windows update issues. The windows update issue, it keeps saying it is going to reboot at 10 p.m. when there are no updates to install. It didn't restart at 10 p.m., just moved the time to 12 a.m.. I used the disable windows update patch from chocolatey package manager to hopefully prevent the notification from popping up. Tell Microsoft releases 10049 or another iso.
Even Microsoft has a warning for 10049
Microsoft urges app developers not to install Windows 10 build 10049 just yet
Actually, You talk like you should not install 3 party software and use what Microsoft provides you. Well Microsoft point from the start with the exception of hardware, all software that works on 7 & above should also work on windows 10.
If my 3 party software didn't work, I most likely wouldn't upgrade ever and a lot of people would follow this. The only thing that has me even considering it, is how quick (Most of the time) windows 10 installs from an upgrade iso. I am still waiting on Microsoft legal definitions of a few items. Here is what I want to know from Microsoft legal. How long my upgraded device will be supported, what happens if I need to re-install, what happens when it is no longer supported? I am not talking about when the device dies, just an assumption a lot people are making. Will 10 become subscription based, if so Microsoft can forget me as far upgrading or buying a new device ever. I don't want waste my time, if Microsoft going to have subscription service after a year-A lot of reputable website are reporting that is possible. I already pay to much for my internet service, which I may be disconnecting by the end of this month. I found out, I really don't need the internet. I have done most things I could with-in a year. Even though I would miss the forums. I stopped using facebook, twitter. I watched all the free movie and tv programs I could fine. Now, I only use forums (Not just here). Pay bills Online, get huge updates for windows 7, test windows 10 build, look up our medical issues. Not sure it is really worth the cost of $40.00 U.S.D. a month.