I never had battery drain/high CPU issues with the shorted charger installed.

The biggest reason for ending my N900+Qi experiment was form factor. Having to go with a hacked reassembled external USB plug (unlike future Neo900 which will have under the battery cover pins or pads for the hacker connection) and exposed ribbon cable made the phone constantly vulnerable to external damage from bumps and pocket snags.
I also had to find a way to secure the receiver pad externally due to fit issues with a Mugen/double Scud battery system. It looked pretty good new but the pad being thin, inexpensive, and attached with room temperature peelable 'sticker' adhesive also began to wear at the edges and eventually unstick from pocket wear, body heat, and the heat of being on the inductive charger. Despite the un-sticking pad problem the ultimate failure and end of experiment was a wear through where the ribbon cable went over and edge between the phone body and where the Mugen cover attached.
I have also found that despite the peril of a USB port breaking fall while charging, which has broken several of my N900s, it is easier to get a reliable overnight charge by plugging in than setting a phone or tablet onto a pad requiring placement within a spot that has about 1cm or less error zone.