When using Rain Dance, Thunder becomes 100% accurate. However, if the foe is to use a move like Sand Attack that lowers accuracy, would the RainDance Thunder still have 100% accuracy?
It goes down. 100% is the new standard for it.
In rain, Thunder skips the accuracy check completely. It won't be affected by accuracy-lowering moves as long as rain is on the field.
Thunder (Bulbapedia)