fighters dont work as laser turrets, they dont nezessarily hit transports if they are busy fighting the attaking figs.

Phase 2: Airfight
The fighters of the two empires in this phase engage in dogfights with each other. As the attackers bombers and transporters have no capability to attack other flying units they just try to hide and survive. The defending fighters have got a natural defense bonus. The maximum loss is 30% of fighters for both sides. The loss of transports and bombers of the attacker depends on the ratio of attacking and defending fighters. So it won't protect your droids in this phase, if you send more transports than necessary. The maximum loss of bombers is 30%, while all transports can get shot down.

So basikally, there is no formula, sinze its based on your attaking bonus and defensive bonus, plus that "natural" defense bonus (probably added to make figruns kost more morale and loses).

"Transport"
Transports are loaded with up to 100 ground units and attempts to land them on the surface of planets. Transports are completely defenceless, and must be protected by air units.     Air defence: 5

This is kontradiktory in the guide, they are defenseless but their air defense is 5

"Bomber"
An offensive unit that is designed to destroy enemy ground defence turrets so that transports are able to land. Every Bomber has got a 10% chance to hit a Laser.     Ground attack: 10
Air defence: 2

"Fighter"
Fighters engage in combat with the opponent's air units; fighters, bombers, and transports.     Air attack: 10
Air defence: 10

^ In that order, 1st they engage figs, any remaining engage bombers, and finally transports.

So in your ezample, if you send 10k figs 1k transports, against 10k figs, theorikally none transport would be hit, but this is false bekause of att/def bonus, from raze and from researzh, 'no fear' bonus, FA tag, war bonus, plus the "natural" defensive bonus for defending fighters. 
The program kan generate 10k random numbers (from 0 to 99) for ur attaking fighters and add +10 to eazh, plus all the other bonus. Then generates other 10k random numbers for defensive fighters and add +12 to eazh (NatDefBonus=2) plus all the defender bonus. Then konfront those 20k numbers and find out how many of ur figs were hit, and how many of def figs were hit.

Now, the program does not generate new random numbers to hit bombers and transports, meaning figs dont fly 2 times.
Lets see it with 1 ezample, you send 5 figs 2 bombers 1 transport, against 7 defending figs:
setting your ezternal bonus as 65% (raze+nofear+FA), and the defender ezternal bonus at 50% (raze only)

attfig1 --> 33+10+bonus=71    vs   deffig1 ---> 45+12+bonus=85      ----> deffig1 wins with remaining 14
attfig2 --> 78+10+bonus=145   vs   deffig2 ---> 55+12+bonus=100    ----> attfig2 wins
attfig3 --> 24+10+bonus=56    vs   deffig3 --->  76+12+bonus=132    ----> deffig3 wins with remaining 76
attfig4 --> 68+10+bonus=129   vs   deffig4 ---> 59+12+bonus=106    ----> attfig4 wins
attfig5 --> 72+10+bonus=135   vs   deffig5 ---> 47+12+bonus=89      ----> attfig5 wins

now
deffig6 --> 36+12+bonus=72  vs   attbomb1  ---> 42+2+bonus=73     ----> bomber1 survives
deffig7 --> 74+12+bonus=129  vs   attbomb2 ---> 26+2+bonus=46    ----> deffig7 wins with remaining 83

now
deffig1 --> 14 remaining   vs  transport1 ---> 45+5+bonus=82     ----> transport survives and takes land
deffig3 --> 76 remaining  (unused, bak to hangar)
deffig7 --> 83 remaining  (unused, bak to hangar)

RESULT of THE battle
2 attaking figs destroyed    ---> if they were more than 30% then this result would be made up to fit the rules
3 defending figs destroyed  ----> same as above, so it will show as only 2 defending figs were destroyed.
1 bomber destroyed   
0 transports destroyed

With this simple kase u see sending a lot of transports does not reduze losses at all, if you had sent 3 transports, 2 of them would mostly have been destroyed by deffig3 and deffig7