Will This Name Come to a Bad End?
You're smart to zero in on the point where first and last names meet. Like intersections in a roadway or joints in a body, name junctions are natural trouble spots. The key is to recognize possible sources of friction.
As you suspected, some names twist the tongue when they bump up against each other. Trying to pronounce a name junction like Herb Frumkin puts your mouth through its paces. Other junctions can lead to letter transfers, in which the listener mistakes where one name ends and the other begins. Kent Racey, for instance, will frequently be heard as Ken Tracey.
When the two sounds at the juncture are the same, watch out for "disappearing letter syndrome." One of the matched pair of letters may vanish -- especially if either sounds perfectly natural without that letter. Philip Palomar is set up for a disappearing P, because Philip Alomar is such a natural sounding name. And yes, Ellis Smith will see an S vanish as he's mistaken for a girl named Ella Smith, again and again. With 20 Ellas born for every Ellis today, it's an all too natural mistake. (And in case you're tempted...nope, you can't fix this with a middle name.)
The S collision isn't necessarily a death knell to your favorite name. On an everyday basis, first names spend most of their time on their own. When a teacher calls on Ellis in class, or a friend shouts to him across the playground, he'll just be Ellis. But if you know that having to say "no it's Ellis, with an s" is going to drive you crazy -- or if you suspect it will drive your son crazy -- you may have to look elsewhere.