funny answer: he's an empath

actual answer: i don't think he "knew" at all actually. i think he guessing. there's no evidence to support that takaya can read minds or gauge peoples intentions or through some other means just Know these things. and it's not really like a weird assumption to make either. you see a guy who's been on the same drugs you've been on for two years, you say yeah well those drugs will kill you eventually. you see a mentally unstable orphan child with nothing but a spear in his hands and rage in his heart and it's a pretty good guess that suicide is on the table.

the alternative (but in my opinion much more unlikely) answer is that he found out through chidori, since we know she has some abilities as a recon persona and we see her infiltrate into SEES' comms. the problem with this is that we never see her able to infiltrate into people's minds, and - even if she did have this ability - there is no instance where she would have been close enough to ken to gauge as such, especially with the consideration that it has been a month since her capture on 9/5, september's full moon operation. again though, if chidori was able to read minds, there would be no reason for takaya to have to investigate himself to find out who on SEES has a recon persona like chidori's. because she would be able to gauge that for him. and in scenes where she's present, takaya still asks shinjiro questions across various instances to get information on SEES' operations.

so yeah he's just guessing probably. i don't think he would've overheard ken making plans like that because ken spends most of his time in his room anyway