Nope cost you nothing. Only slows you income down if he's mass murdering them.

The big danger of losing trade ships is that they're basically free XP for enemy caps.

losing a trade ship temporarily decreases your trade port income rate until the trade ship is rebuilt (takes about 45 seconds). its not a huge amount of credits, but its generally a bad thing if youre opponent is knocking off your trade boats frequently. 

whats worse than your own income loss is that your opponent gets to just blatantly take the credits that were in the trade ship. he gets cash on the spot for blowing up a trade boat. 

Trade ships take 25 seconds to respawn. They produce around .3 credits/sec each, more or less depending on research and the strength of your trade route.

the amount of credits in a trade boat depends on the route it was taking. its usually not a huge amount though, less than 100. those credits are not deducted from the player who lost them, they are only added to the player who makes the kill. what is deducted from the player who lost the ship is a portion of the income provided by the trade port the ship originated from.

for example, if a trade port is hosting 5 ships (the number they host seems to be related to the length of the route, thus longer routes being worth more) and produces 1.5 creds/sec losing one of those ships will reduce the income of that port by .3 creds/sec until the boat is rebuilt. just an example, though the numbers are pretty typical.