So I did some math on the routes based on available runs and videos from youtube.
The most recent being:
http://www.youtube.com/watch?v=_NzL6NEvB7c
This test showed that for the silverscale route (without TAS-optimizing) taking the owl is about 4 seconds faster than travelling down Zoras River.
Firstly this means that for the Goldscale-route travelling down Zoras river would definatly be faster than taking the owl because you can plant the bean before speaking to king Zora. The exact numbers after talking to King Zora are as follows:
1:38 for leaving to Zoras river, travelling down, entering marketplace
2:00 for diving to Lake Hylia, grabbing the owl, and entering marketplace
With both routes getting about the same amount of rupies.
This will save some time for the Goldscale route compared to the Silverscale route which according to the video above goes faster with grabbing the owl.
Maybe with TAS-optimization of the silverscale route it is possible to shave enough seconds off of the Zoras River tactic so that it becomes faster than grabbing the owl?
Any thoughts?