There's an implied level of uncertainty with "indicate". That is, the "likely" , "probably", etc. is implied.

I don't understand why you bring this up. You've already agreed that "a list is likely present" isn't the same as "a list is present". It now sounds like you're trying to prove the opposite. Did you change your mind? Either way, the argument fails.

Our records indicate a depth of 3,000 feet here.

What's uncertain here is the validity of the records. You can't measure the validity of parens.

The map indicates where the treasure is buried.

What's uncertain here is the validity of the map. You can't measure the validity of parens.

That is, the "likely" , "probably", etc. is implied.

The uncertainty would be about the validity of the parens, and that makes no sense. The uncertainty is therefore not applicable to "parens indicate the precense of a list".

There is a relation between the records and the depth: The records were built from measurements of the depth. This is why the records indicate the depth.

There is a relation between the map and the treasure: The map was built based on information about the treasure. This is why the map indicates the location of treasure.

There is a no relation between parens and list, so one can't indicate (point to) the other. This is why the parens don't indicate the presence of a list.