Does installing to an extended partition reduce disk performance?

I think that rather than the logical structure, which should not have any impact on performance, you might be observing a difference in speed due to physical locations of the partitions on the drive. The first partition might be faster than the last one.

The key to a fast boot process is low access speed (rather than transfer rates); this is why SSD will allow you to boot in seconds rather than minutes.

However, the access speeds in a hard drive can vary depending on the physical location that the reading heads need to access; the access speeds may vary as much as twofold. The main reason behind that is that as rotation speed is constant for the whole disk, more area passes under the heads on the rim rather than the area near the center of the plate. Some more information about that here.

Another thing that might influence the access speed is the partition size: the smaller the partition, the higher the speed. Here you will find the results of a test that shows how the performance can drop depending on how large a partition is.