I found the problem.
The GDB-Server couldn't load the .arp file for the chip because the path was longer than 248 characters (**bleep** you Windows).
CMD>CM C:\Users\mdenzinger_lokal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\NXP_MBDToolbox_S32K3xx\tools\eclipse\plugins\com.pemicro.debug.gdbjtag.pne_5.1.4.202109291837\win32\gdi\P&E\supportFiles_ARM\NXP\S32K3xx\nxp_s32k344_1x32x1012k_hse_disabl▒
.ARP file does not exist.
Error loading programming algorithm - load aborted.
Error occured during Flash programming.
Most users probably won't have this issue because theis username is shorter (It's only 5 characters to long).
The workaround for me is to change the MATLAB Add-Ons Folder.
Maybe you could do something about that in future versions of the MBDT