Is there any quality difference between ImageMagick and Lightroom, when converting RAW files (for example, CR2) to JPEG in 100% quality?
There are two aspects to your question, because "converting" from RAW to JPEG isn't a simple thing — it's an interpretive process.
So, your results are likely be significantly different. ImageMagick just uses the rudimentary raw conversion from
dcraw, and doesn't appear to give you much control over that. Lightroom uses Adobe's rather sophisticated RAW converter, and gives a great deal of control over conversion choices.
The second question is whether "100% jpeg" means the same thing in both of these programs, and the answer there is "no, it doesn't". But, at that level, I'll be shocked if anyone can tell the difference visually even with very careful inspection. The filesize may vary, but there won't be any really meaningful difference.