I have a 1999 Honda CRV with just over 200,000km
It usually happens in the morning.
I have to turn my key and it takes from 3 to 6 seconds before the car starts.
I hear a faint humming noise during that time.
The battery is fine, and once the starter kicks in, it starts fine.
It does not usually happen later in the day, just after being parked outside over night - usually 13 to 15 hours of sitting idle.

 

sounds like a fuel pump issue.

Try this turn the key to II and wait for the clicking sound (this is the sound that means your fuel pump is primed). Then engage the starter. It's a good habit to do this every time you start the car.

This might not solve your problem.

 

I have had experience in the past before where the fuel pressure regulator was slowly leaking and would take a few seconds to start...not on a Honda but you could look into it.