I'm trying to understand how can I trust trade bonus:

Is it correct to assume that cost of any item is sum of all basic resources which is used to create it?
If yes, then does it take into account possible productivity bonus? or simple one step crafting with +20% productivity bonus can be as efficient as +20% trade?

Let's try to understand simple exchange:
One market suggest deal: 5 iron stick -> 3 iron ore. And this deal is -15.6%, I thought I shouldn't use it since it is less than zero 0, but I can craft 3 iron ore back to 6 iron stick, therefore get profit. Is it a bug during calculation in this particular case and it should be +15.6%?

That trade overview quality correctly says -15.6%.

Item values are calculated based on four factors:
1. Total item value of recipe ingredients.
2. Number of ingredients in the recipe (giving a bonus to resulting item value due to complexity in crafting).
3. Time needed to craft the recipe (giving a bonus to resulting item value due to number of assembling machines needed to automate production of the given item at a specific rate).
4. Whether fluids and items are used in the recipe (giving a bonus to the resulting item value due to having to tap from a fluid system along with belts, which means at least some form of logistical challenges is involved in producing the item).

"Is it correct to assume that cost of any item is sum of all basic resources which is used to create it?"
No, all of these factors come together to make it so that items with complex production lines are worth exponentially more than items with simpler production lines.

"but I can craft 3 iron ore back to 6 iron stick, therefore get profit."
But how much energy and space are you using to accomplish this, especially if you want to maximize throughput for the market? If you instead trade with the market, you sacrifice material value for building space as well as freed up power on your electric grid, and the market can make that trade in bulk amounts up to a very high throughput. It's starting to sound like a good deal, isn't it? Again, this is purely a consequence of factoring time and recipe complexity into item value calculation. It leads to more accurate representations of an item's true value to you.

"How trade efficiency is calculated?"
The quality of a trade is calculated based on the calculated item values. See an item's value with the command "/item-value <item>". In your iron example, that's "/item-value iron-ore" and "/item-value iron-stick". The command shows that 1 iron ore has the value of 0.05 coins, and 1 iron stick has the value of approximately 0.0355 coins. Again, remember that these item value numbers are calculated based on the factors listed above. Now, if you have the trade 5x iron stick -> 3 iron ore, then that means the amount of "value" that you give in the form of iron sticks is approximately 0.1775 coins, and the amount of "value" that you receive in the form of iron ore is 0.15 coins. The numbers work out such that going from a value of 0.1775 coins to a value of 0.15 coins is a 15.6% loss, not gain.

Thanks for detailed answer!

Is it possible to allow users to configure weight of each factors via mod setting? For example in the late game I have almost unlimited amount of energy, space, and assmeblers to craft staff, but it can lack fresh ore patches (previous are almost dried off or I don't want to spent time to build new ones). So I want my factory to use resource and market deals efficiently. Ideally to run forever without need to build new ore patches.

Currently I can use suggested deals: change raw ore to science packs and quickly ran out of resources compared to usual processing. It certainly save a lot of time and spaces, but overall factory can loose possible output or run dry

There are numerous steps involved in producing science packs, as well as most other items in the game, from ores. This makes it highly inefficient to trade ores for science packs. Instead, it is more efficient to produce the items directly with the ores, and perhaps sell the science packs if you get too many of them. This will maximize the usage of your ores. You are also able to visit The Great Ring of Super Chunks for practically infinite ore. Conversely, if you convert science packs into ore (going the other way from what you described), you get a lot more ore out of what was consumed to produce the science packs. The item value calculation is designed to work this way so that you are incentivized to build a large factory, just like in vanilla. The bonus that markets really provide is getting to sell your excess high-end products or trade them in for other high-end products. Additionally, version 0.4.0 will encourage you to "sell" high-end products like processing units or mark 2 modules to get to the most game-changing feature of all of them (more than markets, more than super chunks, etc.).