Just intonation does produce harmonic sounds; perhaps the most harmonic sounds possible. You are correct that for a Justly tuned system to work, then each of the tones that you use will need to be adjusted relative to the current tonic. Because of this, you are correct to think that there will need to be many different 'flavors' of each note, depending on the context. There has been enormous work done in this field many composers and scientists over many centuries. The source I choose to share here is the work done by the American composer Ben Johnston. This is an example of the notation he used to distinguish between each specific note, and they are created by performing simple mathematical operations (basic arithmetic).
I will give a brief explanation of Johnston's system here, and relate it to your question. Johnston's motivation was to pretend as if Twelve-Tone equal temperament never became a popular trend: he pretended that composers had thought it important to explicitly describe intonation through their notation system. Of course, this is not what happened, so he had to create a system of his own. You could think of his system as a way to get from one note to another without having to explicitly define EVERY NOTE that one would need to use. This might seem confusing, so let me define something that should be familiar: the Major scale.
The major scale is a pattern of intervals that produces notes that can be combined melodically and harmonically to make music. There is a distinct pattern between each note in the scale that you may be familiar with. If our scale is in C major, and our notes are
c d e f g a b c
then the intervals between each note will follow the pattern of whole (W) and half (H) tones below.
c d e f g a b c
^ ^ ^ ^ ^ ^ ^
W W H W W W H
This pattern holds if you are using a piano, where each whole tone is 'equal' to every other whole tone. BUT in just intonation, this assumption does not hold. In just intonation you define EXACTLY what the value of a whole tone is, as well as EVERY OTHER INTERVAL YOU USE!
If we were going to follow Johnston's model, then we would define the intervals using the simplest pieces possible. For musical intervals, that means ratios between whole integers with low values. The reasoning behind this is because that is how a Harmonic series works. From your question I know you are familiar with this concept, so I wont describe it much other than saying that if you want to make a scale with the most harmonic potential, then you will pick intervals from the lowest notes of the harmonic series (shown by order of appearance here):
The Octave: 2/1,
The Perfect Fifth: 3/2,
The Perfect Fourth: 4/3,
The Major Third: 5/4,
The Minor Third: 6/5
These five intervals are enough to make simple harmonic chords! We begin with the octave. Then we split that into two intervals: the Perfect Fifth, and the Perfect fourth. Next, we split the perfect fifth into two pieces: the Major third, and the Minor third (notice how the numerator of the previous ratio becomes the denominator for the next ratio, and the numbers are growing by a succession of 1). Now we just need to split the thirds into smaller intervals so that we can have melodies that can go up and down smoothly.
One of the simplest ways of doing that is to build Major chords that can be 'stacked' into each other. Why major chords? Because it's a fundamental chord within the harmonic series.
1/1 - 5/4 - 3/2
So if we use the major chord as a pattern, and copy it a few times, we can produce a set of the notes within the major scale. By doing this, we're making a very simple scale, and only using three prime numbers: 2, 3, and 5. (Johnston's system can accommodate prime numbers up to 31, and anyone could theoretically extend it to include as many primes as they wish).
If we use the first three intervals of the harmonic series for the parameters of copying the Major chord, we will get a good amount of pitches to make our scale. We start by shifting the pattern up to start on the pitch a perfect fifth (the ratio 3/2) above the tonic.
1/1 - 5/4 - 3/2
3/2 - 15/8 - 9/8
Then we copy the pattern onto the pitch a perfect fifth below the tonic (equivalent to a perfect fourth above the tonic, but it is less cluttered to go below for now).
2/3 - 5/6 - 1/1
1/1 - 5/4 - 3/2
3/2 - 15/8 - 9/4
Now let's name the pitches to give some clarity. If 1/1 is C, then:
f a c
2/3 - 5/6 - 1/1
c e g
1/1 - 5/4 - 3/2
g b d
3/2 - 15/8 - 9/4
or
c d e f g a b c
1/1 - 9/8 - 5/4 - 4/3 - 3/2 - 5/3 - 15/8 - 2/1
This is a major scale derived from C (notice how the ratios from the F chord are now transposed, meaning they are now 'above' C, and the D is transposed down an octave). To complete this explanation, we need to recall the first description of the intervals between and equally tempered scale, which was composed of two intervals: whole and half tones. The scale we just (pun) made is Justly Tuned, so we actually get two</> types of whole tones! The consecutive intervals of the Just Major Scale is:
c to d to e to f to g to a to b to c
1/1 - 9/8 - 10/9 - 16/15 - 9/8 - 10/9 - 9/8 - 16/15
Why is this important? Well it shows that Just intonation, as you noticed, introduces a lot of variety when it comes to intervals. This means you need to pay special attention to how each note relates to every other note. This is hard to do on paper, but composers like Ben Johnston and Toby Twining have been doing it for many years, and so they have much to teach those willing to listen.
In conclusion Bozho, it is not unpractical to compose music using Just Intonation. That being said, it is not easy. If more composers chose to take up the challenge, then we might develop more tools to make the job more efficient. For now, there is still much work to be done.
Cheers!