I think the short answer is yes, the value will do down slightly if it does not have the original 327 (if indeed it is the numbers matching engine). I don't think that the value would drop as much as it would if you were replacing a 396 375hp engine for something like a 350.
If you plan on selling the car anytime soon, I'd simply rebuild the 327 to your liking (i.e. 350 hp) just keep all your original pieces such as factory carburator and intake manifold if you upgrade those to be similar to the 350 hp version.
If you don't plan on selling it soon and want to go the crate motor route, simply hang on to your 327 and include it with the car if you ever sell it, therefore technically the value will be unchanged. Some folks do like the additional torque of the longer stroke small blocks (i.e. 350, 383, 400) so there will be pros and cons with either decision you make. Just need to evaluate the pros and cons and go with the one that has the most pros and fewest cons
I'm sure you already knew that part.
I'm kind of in the same boat as you. My 302 needs rebuilt, but rather than going that route, I'm simply going to pull it and put a fresh high strung 383 in its place. I'll store the 302 for safe keeps and put it back in if I ever sell the car. Its not on its last leg but does smoke a little and I don't want to get into boring it and tracking down 30 over pistons and all that jazz. I'll let the car's next owner worry about that, which will most likely be my son.
Let us know what your goals are with the car that way we might be able to better help your decision.