氵 is left-side water and gives 潜 its core image — going under the surface, like a 潜水艇 (submarine) or 潜伏 (to lie low). Hidden movement through water is the literal sense; "latent" extends metaphorically.
替 here replaced traditional 潛's phonetic 朁 (cǎn) in the 1956 reform — a visual approximation rather than a sound match. The reading qián was preserved from tradition. The modern 替 element has nothing to do with "replace" semantically.
