Two reasons really. The shoulder on the half lap adds a great deal of strength to the joint, especially with 6' posts for trellis panels. Large panels also get a lot of pressure from wind, so the stronger the joint the better. Mainly the posts have to overhang the deck to get the panels lined up along the edge rather than the panels overhanging the deck - which looks awful.
Also I tend to use the 'Easifix' spindles quite a lot because they look good & are so fast to fix. The base rail has to rest on the deck, so the posts have to overhang. Even with square spindles which fix onto the side of the joist, the posts need to overhang to get the handrail in the right place.
Through bolts are the ideal situation, if you plan it ahead, but often you will get customers asking for 'retro fit' panels or spindles and sods law being what it is, the post spacing means you hit a transverse joist, so you can't bolt through.