So I started Iorveth's path. I am just at the beginning where the dwarf shows me my rooms. I finished the fist fighting quests and took the other side quests from the notice board.
But they do not appear in my journal except the harpy queen one.
Is this intended? I am a bit confused.

they are not contracts all, but notices; hence the name. most of it is "flavor text".
you only get the harpy contract form there, the harpy queen quest starts when you get the key to their lair, if i remember correctly. so nothing's wrong with your quest log.

But the other contracts I get as journal entries, For example the Endrega and Nekkar one.

yes, because they are "contracts", so they have quests associated with them. not all notices in the notice board are contracts. some of them are just general notices , so they don't have quests. i really don't know if i can make it any simpler. don't metagame...

This is 100% correct.

I have the harpy queen contract but not the harpy one. Ah well when I get back I try again.

check it again. i bet my not-yet-arrived-dice-poker-set that you misread that...:P