The Honda Indycars look strong so far this year (thank you for not spoiling LB), but as mentioned I think Ganassi has a lot to do with that...plus the Indycars are done by HPD, which has little to no connection to Honda Japan, as I understand things. There's also the new Acura GT3 program which isn't doing terrible (the Shank cars have been pretty competative), but again, that was developed largely in America and Europe.
Honda F1 and SuperGT though, they've been nothing but terrible for a couple years now...and from what I understand, a lot of the electronics are coming from the same place (iirc, the NSX Hybrid from 2 years ago was using the same hybrid system as the F1 car).
I haven't looked too deeply into the whole thing, but during the Chinese GP, I thought I heard someone mention that Honda is using university graduate students to work on their racing programs - like the graduate students thesis projects are various aspects of the racing program. I do know that the Japanese manufacturers have a habit of giving out scholarships to students, paying for their studies, and then have the students be life-long employees for the company....or something like that.
But if this is the case, that Honda is using university students instead of industry professionals to engineer thier racecars, it's no wonder they are where they are.
Watching TCR last weekend, I was very surprised to see the Westcoast Racing team switch from Honda to VW. WC has been a Honda team for a long long time now, haven't they? Strange to see them switch manufacturers.