For joining syllables, LilyPond doesn’t use the hyphen of the text font but instead draws a simple line with variable length. Its standard vertical position doesn’t always fit the proportions of the text font. When using a font with a large x-height, it may be too low.
You can adjust the vertical positioning of the hyphens manually. To get a good result you may want to insert a “real” hyphen for comparision (the l-e in the snippet).