Does marinating fish actually help the spices get in its flesh?
Yes, marinating, or letting sit with a rub (which is what you're doing) does help fish flavor.  

However, for most fish, there's no point in marinating filets or steaks "for hours", since fish flesh is very porous and spices, acids, oils and other flavorings achieve maximum penetration in less than an hour.  The exception to this is dense-fleshed fish, such as swordfish, tuna, and opah, which can be marinated for longer -- up to 8 hours.  Also, if you're applying a rub to whole, skin-on fish, you do want to wait an hour for the spices to "soak in".

The other exception is salt.  There are recipes where you want to salt fish, and let it sit and drain for between 2 and 8 hours to firm up the flesh or change the flavor.

The above is paraphrased and summarized from Jay Harlow's West Coast Fish, and confirmed by my own experience.