Question: It is commonly said in secular sources that the shapes of the trope and nekudos we use today were invented by the [Masoretes](http://en.wikipedia.org/wiki/Masoretes) (7th to 11th Century CE), but I cannot find any source in our mesorah to this effect. 

Is it based solely on the archaeological premise that we do not see them documented historically until then, or are they affirmed by a halachic source to have been invented at that time?

Could it not be an older tradition transmitted and documented by the Masoretes?

The most obvious ramification here is these systems' presence in the Zohar Hakadosh (eg Tikkunei Zohar, Tikkun 69 pg 107a) traditionally attributed to Rabbi Shimon Bar Yochai (d. 2nd Century CE). Either these systems were in existence at that time, are present in the Zohar as a product of ruach hakodesh, or represent later additions to the text.

Answer: 
Rashi on Berachot 62A says that people used to use hand signs to indicate the proper vocalization of the words as the Torah was read. I have heard from several different people, but not seen in writing, that the nekudot and taamim that are printed today are attempts to pictographically represent these hand gestures. This would explain why earlier texts such as the Zohar could refer to the symbols before they were formalized in writing, and why many sources discussing the subject don't see it as a contradiction. This is stated in Wikipedia as well: <http://en.wikipedia.org/wiki/Cantillation#Tiberian_system>
No time to format this, well, but these might be helpful:

a) Jerome did not have it, in his time:
<http://parsha.blogspot.com/2008/02/age-of-trup-part-xxiii.html>
http://parsha.blogspot.com/2008/02/age-of-trup-part-xxiv.html

b) that a gemara says that children had to spend five **years** learning pisuk taamim; and that R' Chanina ben Tradyon taught how to pronounce the Divine Name, because there was not an alternative of writing down the nikkud
<http://parsha.blogspot.com/2008/02/age-of-trup-part-xxii.html>

c) disagreement with nikkud as we have it, from Targum Onkelos and Targum Yonasan:
<http://parsha.blogspot.com/2008/02/age-of-trup-part-xx.html>

d) Yoav's teacher, and timcheh et zecher Amalek:
<http://parsha.blogspot.com/2008/01/age-of-trup-part-xviii.html>