My daughter is now 23. My problem was that when she was young there wasn't much information around. My brother was dysgraphic, but I didn't realise that his organisational problems probably came from the same source. I suspected she was dyspraxic from the age of about 8, but didn't read up on the condition, which was a big mistake. I thought the symptoms were just physical, and so were not that important.
She didn't get an official diagnosis til she was 15 - that was in large part due to my husband's resistance. He was worried that she would "stop trying" if she had an "excuse" for lower performance. In reality, however, she found it a huge relief to realise that the issue wasn't that she was stupid and incompetent (organisationally speaking), but that she actually had a disability, and that it wasn't her fault. The important thing was to emphasise that there were ways to cope with it - work-arounds - and that she still had many strong qualities, such as intelligence, persistence,leadership, and being a caring, compassionate individual.
She did require a good deal of support with organisational issues, and later with some academic ones, in particular how to write coherently and grammatically, which she wasn't taught at school. But she achieved a good 2nd in psychology at university and is now doing a masters in social work.
My brother, on the other hand, was seriously damaged by not having a diagnosis (I don't think dyspraxia, or developmental coordination disorder as it is now know (DCD) was even on the radar back then. Like your son, he could read well, but couldn't write, so his teachers thought he was stupid or "not trying". So yes, self-esteem issues can become a problem quite early. Being kept in to finish uncompleted work would reinforce that.