As mentioned by this [1] eMail conversation, wpa-supplicant itself is faulty in scanning especially hidden networks.
In combination with the current version of connman, this results into the problem that it'll never connects to hidden networks until one scans explicitly by using "iwlist" command.
Tomasz Bursztyka recommended to disable CONFIG_AUTOSCAN in wpa_supplicant, so that connman can use it's own method for scanning networks.
We tested his proposal with the current daisy branch by disabling "CONFIG_AUTOSCAN_EXPONENTIAL" in "meta/recipes-connectivity/wpa-supplicant/wpa-supplicant/defconfig" and now our wifi works like a charm.
After the conversation he also removed his recommendations for setting up wpa_supplicant with this faulty defconfig [2], [3].

Additionally, Tomasz removed the scanning method via wpa_supplicant over dbus at all [4].

All patches are already applied by Patrik Flykt in the connman master branch.

So I see two possibilities:
1. One can disable CONFIG_AUTOSCAN* in the defconfig of wpa_supplicant if connman is choosen.
2. Backporting the patch of [4], so that no changes needs to be done for wpa_supplicant.

[1] https://lists.connman.net/pipermail/connman/2015-January/018691.html
[2] https://lists.connman.net/pipermail/connman/2015-January/018692.html
[3] https://lists.connman.net/pipermail/connman/2015-January/018697.html
[4] https://lists.connman.net/pipermail/connman/2015-January/018698.html