Has it always been this way, or was there a certain time/reason it was classified as not-meat on Fridays during Lent?
The Catholic Church's requirement to fast from meat on Fridays is Canon 1251. The Latin word translated "meat", however, is "caro", which means flesh. Fish is distinguishable from flesh meat by several standards.
Notice in the Gospels that Jesus and the disciples eat fish with some frequency, but are never depicted eating another animal. When Jesus feeds the 5000, it's with a young boy's lunch: five loaves and two fishes.