The speculation driven by the BootCamp additions is rather weak. Being able to boot USB devices from BIOS should be there anyway. It is a rather crippled version of BIOS these days that doesn't have the feature.
Look at the new Ultrabooks being driven by Intel and the Microsoft Surface Pro . Many of the Ultrabooks and certainly the Surface do not have ODDs. So Windows and the vast array of Application vendors out there need to be able to deal with the non internal ODD configurations.
It isn't just Apple that is backing away from DVD. Whether Blu-Ray is a stop-gap is a more significant difference across the respective line ups.
That said, the question whether Apple removes a ODD from the Mac Pro is likely moot. They are extremely unlikely to include two. So at least one is very likely to go. The Mac Pro as DVD duplication machine is extremely dubious value proposition. The number of use cases driving concurrent dual use are very small corner cases.
The primary "shrink down" the Mac Pro needs is only to fit into standard rack horizontally.
Other than that there are more significant uses for the space. Of the candidates:
1. Dual power supplies. (expand the power supply components forward into the ODD bays to squeeze two into roughtly the same size box without cutting power). Or expand the power range.
2. A set of internal 2.5" drive sleds. Or move the 3.5" sleds to the 5.25" space. This either expands internal storage options or opens up more room PCI-e card thermal zone.
3. Move the forward socket array to one of the old 5.25" zones so that don't loose some sockets. [ e.g., if Thunderbolt comes to the back, there is a good chance some other sockets will be bumped from the backs line up. ]
4. A variant on #2 is perhaps locking front facing 2.5" drive slides like what used to be the XServe. Either as USM modules (
http://www.sata-io.org/technology/usm.asp ) aligned with what Seagate is doing with GoFlex or classic lock+sled configurations.
It is pretty hard to use up both 5.25" bays but it pretty easy to find some significant value adds for the at least one.