Ok, silly me did not think about the fact, that Windows and Linux per default have an ARP timeout of exactly 30 seconds as one can see by doing a
netsh interface ipv4 show interface 2
in cmd.exe, where the 2 has to be replaced with the Idx of your NIC, one gets by issuing
netsh interface ipv4 show interfaces
On Linux type
cat /proc/sys/net/ipv4/neigh/default/base_reachable_time_ms
in your bash, to see the default ARP timeout in milliseconds.
So the solution would be to set a static ARP address in order to wake a system through SSH or SMB or whatever. To do this do a
arp -s 10.0.0.200 00-10-54-CA-E1-40
on Windows and a
arp -s 10.0.0.200 00:10:54:CA:E1:40
on your Linux system.