Why are some later Mayan scripts unintelligible to archaeologists, while earlier ones can be read?

Simplification or decadence

First, what we know today about Mayan script is that it was logosyllabic, i.e. there were around about 550 logograms (whole words), 150 syllabograms (which represent syllables) and around 100 glyphs representing names of gods or geographical places. This is considered as an usual evolution of the script, i.e. moving from first relatively primitive logographic script to more advanced syllabic script. Again, as usual Mayan script was first and foremost used for religious, magical, ceremonial and official purposes, i.e. stuff concerning elite of Mayan society. Much less for mundane things like IOU 10 sacks of grain. Such pattern was common in other scripts, languages and civilizations, literacy gradually moving from top to bottom and in that process becoming less ritualistic and more practical, and more simplified.

However, what we do know about Mayan script is a fact that such simplification was never fully completed. If we look at Mayan glyphs, we do see that they are rather complex and elaborate, each of them almost work of art and not something you would use to quickly write down something. Technology of writing was also rather complex. Beside usual carvings in stone, pottery and reliefs, there were some writings on paper, clothes and wood. Later two could be considered as beginnings of more modern "temporary writing" in a sense it was not meant to last for ages, while Mayan codices written on paper were somewhere between stone inscriptions and those made on wood. But, most of surviving Mayan texts are of the higher nature, i.e. they concern religion, astronomy (closely connect to religion) and biographies of rulers or nobles. We could be biased in this manner, because less important texts written on perishable materials tend to disintegrate, but that is what we have now.

Where this leaves us with our main question ? Basically, there could be two answers :

1. Decadence: We do know that scribe caste was highly valued in Mayan society, closely connected with priests, perhaps hereditary. They did have their own schools where the art of writing was taught. In such circumstances, it was natural they would want to preserve their position and prestige, even in the situation when society around them was slowly crumbling. Most likely knowledge what do certain less used glyphs represent was slowly lost, this knowledge rot then moved to those more frequently used. However, text was still needed for religious rituals, and scribes were still being payed to deliver it, perhaps blindly copying it from older artifacts. Significance of message and meaning of text slowly became less important, there were few people left able to read them anyway. Finally, it devolved in ritual ornamentation, tradition passed down the generations and original purpose being lost. It should be noted that this knowledge rot was likely never full, because there were literate priests even at the time of arrival of Spanish conquistadors.

2. Simplification is a second option, less possible but still relevant. First of all, it should be noted that deciphering of Mayan texts is relatively new invention. Relación de las cosas de Yucatán which is a basis on current knowledge of Mayan script was considered as almost useless until Knorozov proposed that Mayan script was actually to a large extent syllabic (not completely logographic and certainly not alphabetic as de Landa thought). Considering that large number of Mayan books from the latter era were lost or destroyed on purpose, but also the fact that in that latter (postclassical) period Mayan civilization was effectively divided into individual cities, it is relatively possible that we currently do not understand text that looks like gibberish. Or in other words, glyphs that look like gibberish are in fact written in evolved system, perhaps moving to complete syllabic system with some simplifications. and perhaps this new and evolving system was not known trough entirety of divided Mayan civilization. It could be local invention that simply didn't spread wide enough. Such things did happen in other parts of the world, with whole Romance group of languages evolving from Latin, and slowly accumulating various differences between them.