The flares should be no more or less obstructive than the normal smoke explosion from the cannon. Period. For being mostly a paid cosmetic, it sure is poor design to have them go mostly unused (and unpurchased) because they put you at a slight disadvantage.
I reckon most people use them once and then they realize it makes aiming your cannon more challenging and are never willing to spend money on them.
I know that when I'm buying a ship set in the emporium, I am definitely not wasting ancient coins on flares.
It's been an ongoing complaint since flares were introduced and I'm surprised they haven't addressed it yet considering the potential forfeit of revenue and wasted dev time.