Sentence One is in fact not Past Perfect, but rather Present Perfect.
Present Perfect: have + V3
Past Perfect: had + V3
Present Perfect is used here to refer to something that started at an undetermined point in the past and continues to be true up to now.
It is unclear whether it will continue to be true in the future.
This may therefore, be commenting on their performance so far with a particular project or task.
I think it is important here to point out clearly that Sentence Two, is the following construction:
They (be) + Adjective
They (be) + V-ing
Therefore, Sentence Two is Present Simple (not continuous).
Present Simple can be used to refer to something that is true right now, but might not have been true in the past and might not continue to be true in the future.
It can be used to refer to something that is accepted as being always true, including scientific fact.
It is cold. (right now)
It is cold in Alaska. (always)
Sentence Two, I think, refers to the people's characteristics. 'They are disappointing' like 'he is annoying', refers to the type of person (or people) that they are, and is therefore always true.