Annoyingly, in Minecraft you cannot change the volume of the thunder sound. You can only switch it on or off. In Survival Games having the sound on is often helpful because it informs you that a player was killed and gives you the direction even if you don't see the lightning strike. During the thunderstorm world event however, there is a constant thunder blasting at full volume so I usually turn the weather sounds off. My suggestion is that you make the thunder silent and play the sound effect as a regular weather sound instead so it is affected by the weather volume settings. You could either do this for all lightnings or only for lightnings from the thunderstorm world event.