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Assume that a conlang is written partially with an alphabet and partially with pictograms. The idea is to have something like the Japanese writing system.
Does it follows the structure of natlangs to have symbols for the words which are of particular cultural importance for the speakers of this language? Is there a common pattern or system for a categorisation of words which have their own symbols in most of the natlangs using such a mixed writing system, e.g. man, woman etc?
There is already a conlang that kind of does that. In toki pona you can write the words in a set of pictograms (actually, there are several pictogrammatic writing systems, I'm referring here to the 'hieroglyphs' from the official book). As there are only 120 words, it's easy to have pictograms for all of them.
The only problem is what happens with other words. Names, for example. The toki pona solution is to select a hieroglyph whose word starts with the respective sound. This leaves some choice, as you typically have several pictograms available and you can choose a word whose meaning is somewhat relevant to the name. For example, Kanata (Canada) could start with the pictogram for kasi ("plant, leaf"), to link to the maple leaf; Nokisi (Norway) would start with nena ("hill, mountain"), etc.
Here you are using pictograms to spell a word, but it is easily conceivable to have a separate script for names and foreign words.
If the vocabulary of your language is substantially larger than toki pona's 120 words, you might not want to use pictograms for everything. In this case you could use them either for 'core' words (whether you define them by meaning, age, etymology or frequency), or it could be words that have no inflections (and thus don't change, eg function words like and and for in English).
In the end it's your choice how you solve this, but there are certainly some possible justifications for different choices that you could explore.
One consideration is the source of the symbols themselves. DINGIR had the syllabic value /an/ in Sumerian, but it also stood in for the word "god" because An was a Sumerian god. (And, one step further, DINGIR still meant "god" in Akkadian even though the Akkadian word for god was now ilu.)
The Sinaitic inscriptions were written in an abjad, and yet (may have) used certain letters as the words that the letters were derived from: For instance, the glyph ʾ may have stood for ox (* ʾalp), h may have stood for celebration (* hillul), and r for head (* raʾsh), because the pictures that originally formed those letters depicted an ox, celebration, and a head.
So if your script derives some of its symbols from pictures of something, the symbol could stand in for the word that the glyph depicts (or once depicted). This is a little circular when trying to determine which words should have their own symbols, but the point is that what determines which words have this status is often just an accident of history instead of a categorization of important words.
