Prior to Xehanort the heartless had trouble leaving the Dark realm which is why they was practically unheard of till between BBS and KH1.
Plus we've seen how the heartless travel, dark corridors, so I'm doubtful on the portals part.
Them being manifestations is spot on though. Heartless are born from darkness of heart, they are that darkness manifest.
As for how they got there in the first place I'd blame that on the keyblade war. People were consumed by darkness on universal scale and if you notice the legend points out darkness was "born" during the war yet it's also said the Xblade was half dark and half light.
Darkness can't be born of it already existed in some form like within the Xblade. So maybe what was "born" wasn't darkness but the heartless which are "darkness made real".
Got side tracked. xD
What I mean is yes it's likely that heartless were born there as people gave into darkness just like it's likely nobodies were born in the in-between realm. Xehanort upset the "status quo" though and now they all roam the Light realm in mass when before they were fewer than scarce.
