Get a Vti-R over a Si, much, much nicer engine (and other features).
I have an auto Vti-R and have not had a hint of transmission problems, it is now up to 172,000km and shifts like a new car. I change the trans fluid ever 40,000km, which I think can be the reason for premature failures, off the top of my head, Honda recommend a lot more distance between trans fluid changes.
Provided there are no problems currently with the auto (make sure you test it when cold also) and you treat it well with proper servicing, there shouldn't be any problems.
I love my auto Vti-R and would never change it to a manual, you just need to remember the Prelude is more of a 'cruiser' than a 'sports' car, I do a 700-800km round trip about once a month and it is brilliant for that sort of driving.