I would like to upgrade a carbon fiber bike (Scott CR1) to Ultegra Di2 with internal wiring. Can I drill a hole where the cable holders are located (one next to the fork, one near the bottom crank & one at the rear, close to the derailleur) in order to route the cables inside ?
This is one of those questions where if you have to ask "should I do this?", the answer is "no". Carbon frames need to be specially reinforced (during manufacturing) in the areas that drilling takes place see, for example, this discussion, and you could create stress concentration points or otherwise compromise the integrity of your frame.
The words "catastrophic frame failure" are not ones that you want to hear, particularly from your hospital bed.