I think I found the problem.

Instead of copying files to the new user home I hided some directories
(chown to root and chmod to 700).

Here is a list of the directories in my home with number of files and
size.

opt: 12912 files / 349M
bin: 168 files / 1.9M
data/Desktop: 498 files / 6.1G
data/Documents: 306 files / 78M
data/Download: 39 files / 703M
data/Misc: 17 files / 11G
data/Projects: 10087 files / 435M
data/Public: 0 files / 0M
data/Resources: 219017 files / 22G
data/Software 2196 files / 8.7G

I could avoid nautilus' high CPU load after hiding data/Projects,
data/Resources and data/Software. Un-hiding these directories step by
step again increased nautilus' CPU load and nautilus UI usage latency.

My first guess was that nautilus simply has problems with directories
containing a lot of files. On the other side the directory 'opt' had no
impact on the problem.

The actual problem with 'data/Projects', 'data/Resources' and
'data/Software' was that I configured my '~/.config/user-dirs.dirs' like
this:

XDG_DESKTOP_DIR="$HOME/data/Desktop"
XDG_DOWNLOAD_DIR="$HOME/data/Download"
XDG_TEMPLATES_DIR="$HOME/data"
XDG_PUBLICSHARE_DIR="$HOME/data/Public"
XDG_DOCUMENTS_DIR="$HOME/data"
XDG_MUSIC_DIR="/mm/Music"
XDG_PICTURES_DIR="/mm/Photos"
XDG_VIDEOS_DIR="/mm/Videos"

After setting

XDG_TEMPLATES_DIR="$HOME/data/Documents"
XDG_DOCUMENTS_DIR="$HOME/data/Documents"

and running

$ xdg-user-dirs-update
$ xdg-user-dirs-gtk-update
$ killall nautilus

the problem was away, also if I un-hided the 3 problematic directories.

So I guess because nautilus considered '~/data/' as a document folder,
it did something it does not do with "normal" folders - whatever it did,
it could not handle the large number of files within '~/data/'.

-- 
high cpu load on startup and when mounting
https://bugs.launchpad.net/bugs/239167
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