To calculate Evade, all Evade-boosting bonuses are totaled multiplicatively. So, to calculate how much Evade your ship will have, you can use the following formula, where x, y, and z are percentage-based Evade bonuses that have been converted from a percentage to a decimal (i.e. 30% = .3):
Evade = 1 - [(1 - x) * (1-y) * (1-z)]
So, in the case of an R5 Stingray (30% Evade built-in) to which you're adding Guidance Scrambler III (40% Evade) and one Evade Upgrade (15% Evade), the formula would look like:
1 - [(1 - 0.3) * (1 - 0.4) * (1 - 0.15)] = 0.643, or 64.3% Evade
Accuracy, on the other hand, is totaled additively, which is much easier to calculate. You can use the following formula, where x and y are percentage-based Accuracy bonuses that have been converted from a percentage to a decimal:
Accuracy = Base weapon accuracy + x + y
So, in the case of a Siege Missile D55-E (50 Accuracy), which you're adding to an R5 Vindicator (+20% Accuracy) with the Missile System III special (+40% Penetrative Accuracy) equipped, the formula would look like:
50 * (1 + 0.2 + 0.4) = 80 Accuracy
Note here that this allows Accuracy to exceed 100; this is correct. However, an Accuracy greater than 100 will only matter when being used against an enemy with Evade.
When calculating how Accuracy and Evade interact, the attacker's total Accuracy stat (which is treated as a percentage) and the inverse of the defender's total Evade stat (also a percentage) are converted to a decimal and multiplied together:
Chance of successful hit = Accuracy * (1 - Evade)
So, in the case of the above Vindicator (80 Accuracy) attacking the above Stingray (64.3% Evade), the formula would look like:
0.8 * (1 - 0.643) = 28.56% final hit chance
These formulas for Evade and Accuracy can be applied to understand the hit chance of any weapon in the game.