I've always found it strange that Ran suspects. Let's say your best friend did that I mean it's not natural to shrink, it would never enter your mind to think hey is this little kid my best friend unless he went up and told you hey dude I shrunk. But if he's trying to hide it then there's no reason even for a second for Ran to believe that Shinichi is a kid. It would be easier for her to think hey that kids a lot like Shinichi when he was a kid. It's like if I thought man my friend is weird I never see him on a full moon and he goes on and on about eating children, wouldn't it be easier to think he's a psycho who eats children on the full moon rather than believe he's a werewolf. I guess what I'm saying is if you hear hoof-steps it's probably a horse not a unicorn.
Though I firmly believe that Ran knows that Shinichi is Conan, but because it's so strange and because she doesn't want to, she doesn't believe it.