'data remove' does not delete tag, instead 'zeroes' it.

Attempting to delete a compound tag does not delete its children, attempting to delete a child merely changes the value to 0.

How to recreate:

'/summon ender_crystal ~ ~ ~'
'/data merge entity @e[type=ender_crystal,limit=1,sort=nearest] {BeamTarget:{X:100,Y:100,Z:100}}'
'/data remove entity @e[type=ender_crystal,limit=1,sort=nearest] BeamTarget'
'/data get entity @e[type=ender_crystal,limit=1,sort=nearest]'

Notice the beam still exists, and the nbt still has the BeamTarget tag, with the appropriate unmodified children.

Attempting to remove the children simply 'zeroes' the values:

'/data remove entity @e[type=ender_crystal,limit=1,sort=nearest] BeamTarget.X'

Thus there is no way to remove the BeamTarget tag that I am aware of, aside from deleting the entity.