Difference between a letter/short article and a full length article?
In my experience, there is no real difference between "full" articles and "short" articles except for length.

Many journals, especially more recent online-only ones, do not bother with this distinction at all.  An article is simply as short or as long as the article turns out to be. Even with journals that do make the distinction, it often has little impact of the de facto length of the material once supplementary material is included---all that is affected is the fraction of the published "iceberg" that is "above water" in the main text. The peer review process is generally the same, and the perceived value the same, just simply some are shorter than others.

In terms of visibility and citations, short articles are typically just as visible (as you have noticed). I have never seen a citation attempt to distinguish between short and full articles, and most citation formats have no way that one could do so. For those who are affected by publication statistics (e.g., impact factor), that's not affected either: these are calculated by journal, not by article category within a journal.

In short: some things are just shorter than others, and that has little effect on their significance.  The editor thinks your article will work better in "short" than "long" format, so take their offer or risk rejection pointlessly.