Considering that the majority of code is written by people who don't know Chinese characters, it would result in never-ending issues, pretty much everywhere.
Korean actually has a two-way system in Unicode. Every conceivable character (= syllable) possible in modern Korean has its own codepoint, which allows most software to display them correctly: from their point of view, it's just another CJK character.
On the other hand, there is a Unicode area containing Korean sub-blocks ("jamo") that were used historically. In theory, you can combine them and get some pretty funky archaic syllables. Almost no software renders them right.
I dread to think what an enormous mess would result if every character was represented as a build-it-yourself instruction manual rather than allowing font authors to correctly represent the characters. This is also ignoring that (depending on the font style), the apparent strokes for a character can change between fonts in the same language (this is because the computer font stroke style and the written font stroke style can be different) -- by putting stroke decisions in the encoding you're introducing a layering violation since fonts should be deciding how characters are styled, not encoding format committees.
Also nobody in China, Japan, nor Korea would switch to an encoding system so incredibly inefficient that more strokes results in more bytes being necessary to store the character (they already compromised with having 3-byte UTF-8 characters when JIS, GB, and Big5 all only required 2 -- and Japan was basically forced to compromise on Han Unification). This would've resulted in the failure of Unicode's mission to be the One True Encoding Format.
Currently stroke-based systems are used for calligraphic effect. You could generate new font types, e.g. bold., but controlling the shape of strokes.
Stroke systems are important for teaching character writing because the drawing order is rigorously prescribed. Once you learn the first couple hundred, you can pretty much guess future characters. Wrong order characters often look bad and suggest a non-Chinese speaker mis-copied them. (e.g. some tattoos)
There are somewhat more sophisticated systems which define both the rendering and stroke decomposition of characters (e.g. CDL: http://guide.wenlininstitute.org/wenlin4.3/Character_Descrip...). The general workaround for characters that aren’t on Unicode would be to use one of these stroke description systems to create the character, then render it to an image and insert it.