The H39 is worth returning to with a higher level crew so you can see the difference in the ship, not to mention for most who have played Fleet league such as myself preping in a BB4 or PCA is habbit and as such we get a chance to have at times a love hate liking of our ships.
The H39 is much better at higher levels again like i said before it still has issues but they are not as noticable unless someone is rushing you and they have armor or a small hitbox when rushing you.
Now the H41 is still a good ship, it has more AA, another support slot, some more DP, can carry another bind of ammo and such over the H39. It is meant to help you grind to the H44 and be preapred for that ship so your not a support down. It much like the H39 can be quite good you will need to practice with it and learn the ship so you don't over extend your ship beyond it's current capabilities.
Either way do enjoy the H41.