The best way to understand "honoka" as "dim" -- and the reason that "secret" is the right choice for the translation into English -- is because the word refers to how clearly something is noticed by others. The word deals with perception, not with potency.
I kind of saw that definition (わずかにそれと認められるさま。かすか。
going more with perception by the physical senses like hearing and smell, etc.
I see things like this (relating to emotions or mental functions like memory) as applying the second definition, of feelings being unclear or not concretely defined (心や意識がぼんやりしているさま。かすか。
It even uses 'feelings of love' as an example for this in the dictionary (仄かな恋心, which I think was what they used for Elena's feelings towards Tseng as well).
I've had it liked to 淡い恋心 before, which is more of a 'light' love. Like the first stages of love before it develops into something more serious.
The trouble I see with 'secret' now (meaning it just came into my head while writing this so isn't too thought out) is that ほのか still refers to it being perceived, if only very slightly. How would 'secret(ly)' work if no one was aware of Cloud's feelings? Even if something is 'dim', it's still being noticed by someone. I woudl think 'secretly' would mean no one knew about it, which doesn't seem to be the case with ほのか used for perception.