Stan, fugues are the classic examples of through-composed music. Are they disorganised? Is it hard to identify their themes (or subjects, as the case may be)?
Not normally, I would think, when in the hands of composers who know what they are doing.
In general, the word "relatively" in your definition applies: fugue episodes, for instance, generally make use of motivic materials from the exposition. There is thus repetition, but it is usually subject to some variation. This is normally also true for through-composed works that are freer than a fugue. Expressionist works of the first quarter of the last century (e.g., Schoenberg, Bartók, Eisler, etc.) tended to be through-composed, but the motivic work was typically very dense, i.e., much use of motifs to bind the works together.
Similarly, the word "relatively" applies to the degree that a through-composed work cannot be divided into sections. Some of Bach's fugues suggest formal sections (WTC I no. 6 has a pronounced binary layout, for instance), and Hanns Eisler's (free atonal) piano sonatas usually at least suggest a recapitulation of thematic materials. At the other end of the spectrum, you have a tour de force like Schoenberg's monodrama Ewartung, which is essentially athematic, yet holds together very well.
All of this should suggest that the concept "through-composed" covers a spectrum, from works that give some impression of sectional division and thematicism to works that have practically none. The common denominator is that they generally give an impression of being written as a single gesture from start to finish.
People have been writing through-composed music since composition became a thing: there are many, many examples in Medieval and Renaissance polyphony; there are examples being written still, even as we speak. In the hands of people who know what they're doing, they can be clear, well-organised works.