1) Any advantages?
Well you eliminate the need for a whole other chassis. Extra line card(s) for 6500 to provide server ports likely less expensive assuming you only need to acquire 6500 line card(s) rather than whole 4500 chassis and its line card(s). Besides possible reduced CAPEX also possible reduced OPEX.
You could provide a lot more performance connecting to the 6500. The original 4500 series only provides 6 Gbps per slot and the dual uplinks, especially if only gig, might be a bottleneck to the core. On the otherhand, depending on what cards you're using in the 6500, you can have up to 40 Gbps per slot and local line card routing.
As to best practice, I don't see a need to install physical layers unless there's a real need to do so.
2) Fiber vs. copper
The other posters have touched on the advantages of fiber vs. copper. Of course, it often is much more expensive, not only the port itself, but don't forget the required converters. For just a couple of uplinks, the incremental cost of fiber isn't too bad unless you need to purchase a whole fiber port line card to provide just a couple of fiber ports.
If you already have copper ports available, you can always start with them and move to fiber, later, if needed.
Also keep in mind the expense of changing your cableing plant. If only copper or fiber runs are already in place, it be might be more costly to add other media type cable to "save" on a line card port type. (With you're diagram, this might not be much of an issue.)
