As the question states, if a creature has blindsight, do they have disadvantage on a target that is within the range of their blindsight and not otherwise hidden/covered?
The wording of the invisible condition suggests that attacks against an invisible creature have disadvantage AND the creature can't be seen without magic/special sense not BECAUSE the creature can't be seen.
Invisible Condition
An invisible creature is impossible to see without the aid of magic or a special sense. For the purposes of hiding, the creature is heavily obscured. The creature's location can be detected by any noise it makes or any tracks it leaves.
Attack rolls against the creature have disadvantage, and the creature's attack rolls have advantage.
Best Answer
The Special Sense Blindsight bypasses the mechanics of being Invisible
The Invisible condition states (emphasis mine):
Blindsight is a special type of sense, along with senses like True Sight and Tremorsense.
The condition explicitly calls out that there are special senses that bypass the condition. As Blindsight allows a creature to see the unseen, being invisible is bypassed by that sense and thus the mechanics that the Invisible condition provides are not activated.
Jeremy Crawford also provides some support:
Once you can see the creature the effects of being Invisible are no longer active.