I love the little linguistic shortcuts crosswords enjoy, and 'kernel' is a perfect example of one of those shortcuts. In everyday speech 'kernel' tends to mean the inner, most important part of something — think 'kernel of truth' — and crosswords capitalize on that strong, ready-made association. Editors and setters like words that have a tight cluster of common synonyms ('core', 'nub', 'gist', 'seed') because those synonyms map neatly onto short grid entries and make for clean, solvable clues. So when you see 'kernel' in a clue, it often points to the idea of centrality or essence rather than a botanical seed, unless the surface reading steers you another way.
Etymology helps explain why 'kernel' leans coreward: historically it comes from Old English for a little grain or seed, and seeds are literally the innermost, generative part of a fruit or plant. That physical image migrated into metaphor — the 'seed' of an idea becomes its 'core' — and crosswords exploit that metaphorical economy. In cryptics you'll also see setters play with both meanings: 'kernel' could be clued as 'seed' for a literal insertion or as 'core' for a straight definition.
On top of meaning, practical factors make 'kernel' a setter's friend. It's moderately common, contains useful consonants and a vowel pattern that fits many crossing words, and it offers multiple cluing angles (botanical, figurative, computing). So when I fill a puzzle and hit 'kernel' as 'core', I feel that nice click of language logic — it's compact, sensible, and a tiny reminder of how words travel from the orchard to the abstract, which I always find oddly satisfying.