I have found more evidence to back it up!!!
Notice how much Heiji will do to see Kudo. He travels to Tokyo most of the time just to see Kudo. For example, in 'Reunion at Mycroft', Heiji shows up only to get a chance to see Kudo. I mean, he was obsessed enough to travel all the way out to a deserted mansion for an event he didn't even like to get a stinking chance to try and see a guy he met once. Don't you find that adorkable? (that word is perfect for Heiji. ^^) And then White Murder, 'I wanted to see you' with a heart on the quote! A heart! A heart! (he only retracted the statement to keep from being tranquilized. *nods*) The Naniwa Serial Murders, he lends Shinichi his special good luck charm and while Heiji used to let people commit suicide, he almost got himself killed to honor Shinichi's words. (adorkable I tell you!) Oh, and there had to be a reason Kazuha thought 'Kudo' was a girl, doesn't there? Wouldn't that mean Heiji talks about Kudo like he would a girl he likes? *blushes* I need to know what he said to Kazuha about Kudo. I must know now. Next mystery!
'The Case of the Separated Lovers' (Files 211-214), like always, Heiji and Shinichi are perfectly in sync. It's adorable! In 'The Spider Mansion' case, Heiji is so happy when he finds out Kudo's going to be there! He's like (wait a second, if this guy is here, then- KUDO! *hugs* (the hug happened. Gosho just didn't draw it. LOL XD) 'The Desperate Revival' arc was Heiji running from Osaka the moment the term was over to make sure Shinichi was okay. (Awesomeness.) Then he even took the time to dress up as Kudo to protect him. The Mermaid Arc has ShinHei! (a somewhat rarer occurance) Shinichi's so worried he stalls the deduction to wait for Heiji. (I don't care that Heiji saved Kazuha. Any person would do that for a childhood friend. I mean, all the Gosho guys would do it for anyone if you think about it. Heiji got himself shot to save a police officer. It's not that different.) In 'K3', there has to be more reason to think Heiji's having an affair other than 'Are you alone?' and 'Is it okay now?' (and why does Kazuha count it as an affair if she isn't even dating Heiji? Sheesh, get a grip on yourself Kazuha. You're not the only girl in his life. Or guy for that matter.) There had to be something more romantic. XD
In 'The Knight of Naniwa', Heiji brushed off his precious kendo match just to beat Shinichi in solving the case. (I know when the guy I like is near me, I really want to beat him in something just to prove something to him. I don't know what. It's just... adrenaline.)
I think that's enough for now... I'm not even halfway through... But I'm done for now.