After starting to use version 6.0 I've had serious issues with performance. Even typing code can be very slow and PhpEd might miss a lot of typed letters while thinking something.

Debugging is so slow that it really affects my work performance: it might take many seconds to get information about variable contents, etc. It just took me 6 seconds to remove a breakpoint. I think it was due to IDE to take that time to get responsive after hitting a breakpoint.

If there is any solutions, I would really appreciate them.

Check your project tree for overheads/unneeded copies of the same files/unnecessary libraries and make them all hidden.
Make sure that your project (ppj file) is on local disk, not on the network
Open Task manager and look for the process that uses CPU and Memory too much. If it's not PhpED, you may want to close it. If it is PhpED you may want to wait until it gets the project parsed
Install more RAM (3GB for 32bit OS or 8GB for 64bit one)

How do I make items/libraries hidden? The project tree is very clean since file versions are handled via SVN, there is no duplicates around. some libraries I could hide for sure, not all of the files are in use all the time.

Ppj file is on local disk and Task Manager says that nor CPU usage or memory usage is near its peak. There is more 800 - 900 Mb of memory available and during these delays processor usage is around 25 %. To me it seems as the problem is in drawing the debug window for globals, thou it does not help to close that window.

25% cpu usage looks like you have quad-core CPU and one of the cores is dedicated to a thread which takes 100% of its performance. So, it looks like the PhpED parser thread is busy. It may explain the delay.
As of how to hide directories and/or files - check the project properties. It's where you'll find Hide Directories input. Add a name or relative path here, or list of names delimited with semicolon. By default it hides only .svn and CVS directories.
Then click refresh in Code Explorer and wait until CPU usage goes down to 13% or below.

Actually I think I only have two cores, since Task Manager only shows two CPU Usage History views.

Hiding directories like that does seem to be very not user friendly way to (try to) go around this problem. I have a lot of directories I could hide, but this way sounds way too time consuming specially, when I need to change hidden folder quite often to debug different parts of our program.

I hid 4000+ directories containing around 8500 files (including SVN's directories and files) and had around 780 directories to work with (again, including SVN). Hiding all those dirs did nothing to performance.

I don't think I had this problem before 6.0 so something has changed to worse.

I just checked a typical Magento project and that contains over 18,000 files with 4,696 folders. I haven't hidden anything and have not had any performances issues at all with PhpED 6, so something does seem to be going wrong for you.

I remember a long time ago I had performance issue with one of the 5.x versions and I ended up deleting the ppx and ppd files from the project folder. When I next opened the project with PhpED, those files were re-created (which did slow things down for a little bit, but I could still work) and the problem went away.

The list of directories to be hidden - may contain wildards like for example *IMAGE* or IMG_*, it's not casesensitive, if you hide a directory, all its content and all subdirectories in particular will be hidden, and finally it may contain relative path or just name. For example .svn;CVS will hide all .svn and all CVS directories with their content, regardless of the place where they apprear in the project tree. If you add MEDIA/IMG, it will hide IMG directories that appear inside MEDIA.
As far as I know, normally people add 5-6 entries to this list to hide backups, minimized js files, encrypted php files, directories created by source-control systems, and so forth.
As of debugging different parts, you may want to split these parts into corresponding number of projects. If you work with Apache or IIS, you don't have to have the project root matching web document root. Project may start in an upper and contain document root as a subdirectory or may appear in a lower place - a subdirectory somewhere inside document root. It's flexible enough and would allow you break your project into smaller parts.

As mentioned before hiding directories did not solve my problem - the lag is still there - and I didn't have this problem in 5.9.

It might be a long shot, but did you try deleting the ppx and ppd files so that they get recreated? All I know is that it did help me in the past.

Yes, I tried that too. Didn't help.

I've also tried to unload all other projects, removing all other projects from workspace and doing these with and without restarting PhpED. No luck so far.

This might be getting into the debugging area, which Dmitri might prefer to be done through support, but ...

Which Windows version are you running?
How much memory?
What release of PhpED?
Local files or network share?
Does a smaller project also have problems?
Do you use any version control systems?

I doubt anti-virus has anything to do with it, but if you haven't tried disabling that then you might want to do a quick test with that disabled. I'm actually a little suspicious that PhpED might be hitting some specific file(s) that are causing it issues. I remember someone saying that had problems with PhpED trying to parse git files.

I think I found something and now I have a suggestion to make: the problem seems to be that there is a lot of data in variables (+10 Mb) and the delay seems to be caused by parsing these arrays/variables. A settings for "Ignore these variables in debug" where one could choose which variables are not parsed in debug might help me out a lot.