You're totally right about that. Different speed screws up your aiming. Different range doesn't matter.
To answer your question, I think the computer calculates the avg. speed and and uses that speed for the aiming control thingy.
It could also be it uses the fastest or slowest speed, but I think it's the avg.
For a good way to make up a perfect setup with different guntypes I sugest this link and download the Excel file and, if nececary, the excel viewer.
You can select the guns in a list and it shows all kinds of stats about them (Energy useage and such) and what the stats are if they are combined.

To all the n00bs I've flamed before...
- Have You Been A Hero Lately? -
The Titan Flies Like A Cow

there are two types of speed ,projectile speed and refire rate
each has its own effect

it's the projectile speed that changes where the little plus thingy shows up on ships you are shooting at. If your range/speed are matched for all your weapons, then all your weapons hit or miss depending on how good you are. If your refire rates are missmatched then all it does is kinda make surges in the damage inflicted.

"On this ship you are to refer to me as Idiot, not you Captain. I mean... you know what I mean."

Refire rate does not affect aiming. A 4.00 refire gun with a speed of 600 isn't going to aim any differently than an 8.33 refire gun with a speed of 600; it just fires less often. The only difference is that you can't use the slower firing weapons in "spray-and-pray" tactics; you have to place your shots a bit more carefully. You could very easily use 8.33, 3.03, 2.00, and 4.00 guns on the same ship, so long as they all have the same projectile speed.

And actually, it doesn't matter too much as long as the speed is CLOSE...for example, a 750 gun and a 700 gun will be close enough together that they will both hit the target, despite the different speed.

----------------------------------------
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Rockets: $100,000
The look on that pilot's face when you launch a full pod of screamers up his tailpipe: priceless
-->In 60 years, I wanna be one of those cranky guys sitting on his porch with a shotgun, yelling at the fools to get off my lawn...

There is the issue of different weapons doing different amounts of damage to different shields. Some weapons do 30% less damage (standard unmodded game) to some types of shields so mixing them may not offer you the best damage ratio but you would at least damage all shields.

Good weapons against one type of shields can be useless against another type of shield. A point worth considering when you move from one system to another and keep the same weapons.

Giskard