While testing MC-203638 I noticed minecarts would become invisible while looking in the general direction of the minecart.
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Does MC-202132 explain your issue?

Yes but my entity render distance is set to the default of 100%. Setting it event higher to 500% does not fix the problem. MC-197328 is the open ticket.

It seems like this ticket is a duplicate because it appears to happens with all entities. However I dont think it is caused by low entity render distance.

Interestingly it only happens to the most recently spawned type of entity. If I spawn a bunch of turtles they will all be affected. However if I place an armor stand the turtles will cease to be affected, but the armor stand will until I place/summon a different entity. If I spawn a squid and then a turtle and then two more squid only the last two squid are affected. Very strange.

I think my entity distance assumption may be wrong, please provide the findings in a comment on MC-197328.
This only happens to minecarts fully submerged in water. Does not happen on fabulous graphics, but does on fast and fancy.