Ah, a explorer explore worlds, a Scout explores stars and watches your borders.
So a explorer is more like Federation ship on Star Trek, a science vessel, that you put in orbit of a planet and you explore it like in Eador when you use a hero to explore a province.
A Scout is faster and also stealth, so you are likely to use it to visit stars and watch your enemies so you know where you can expand.
EDIT: In StarLife we have set 4 types of ships, one of them is recent.
Explorer like I explained above is necessary to explore worlds, thus trigger events and also increase the amount of land your colonists can use. Pretty much like in Eador, but the events are more like those in King of Dragon Pass.
An explorer can go to neutral and friendly territories.
Scout can go anywhere, have the best radar/sensor range, detects attacking fleets and also helps your attacking fleets to infiltrate enemy territory as well as helps spies to infiltrate other empires.
Military can only go to friendly territories, that is because to attack you have to use the Attack Plan, you set your objective, your target, your fleet and where to return after the attack. So the game takes care of getting all your ships together and travelling into the enemy territory.
The enemy can spot your attacking fleet or their spies can learn about your attack plan and then make a Defense Plan, otherwise you are going to reach them unnoticed.
Transport is the last type, it's important because of how we set FTL in our universe.
FTL is possible, however at the start of the game it requires a huge engine, power source and a powerful hull so the ship can withstand the travel. So non-FTL ships are very small compared to FTL ships.
Transports are then the only way to transport goods/food/equipment/non-FTL ships to other solar systems.
So in the game you can plan the route where the transport will go, and it enters a loop.
This also works on how you can colonize planets, instead of making a colony ship, your population will start to migrate to other worlds on their own, you can make an advanced post or starbase there to help them, you can give incentives for them to go there or even pay them to help build the necessary infrastructure.
So the transport ship is very important since without it your population simply can't reach other places.
Because of the nature of FTL, ships are very expensive and you are likely to have a small fleet, since you can't mix the types like 'explorer/scout/transport with guns', then you have to think very well on how many ships of each type you will maintain.
Your empire will also grow slowly and within it's borders as opposed to the famous 'gold(colony) rush' of every other game in the genre. Your empire can't grow too much either, if it grows then it will likely end up splitting into two empires.