My feeling is that, all else being equal, usually the multiple homeworld starts make the game easier rather than harder. On lower to middling difficulties in particular.
But I really have to qualify THAT by saying that it dumps the work of 2 players onto you instead of one player. You've got more territory to manage, more ships to manage, more resources to figure out what to do with, etc. Quite frankly it is usually more than one person can handle at the default speeds on higher difficulties in particular, so you wind up needing to pause a lot to issue orders before the AI can react.
If you do that sort of pausing, then you have the power of two players at your disposal, but with the coordination of one single player at the helm. In multiplayer the AI doesn't scale quite linearly in difficulty with the number of players, because multiple players are almost always less coordinated than one. The difficulty scaling curve takes that into account, but with a multiple homeworld start that isn't the case -- not being coordinated with yourself isn't the problem, but not having enough time to manage all your fronts and economy and such in realtime IS.
So... my answer is that it really really depends on your playstyle. In some ways multiple planet starts are harder, in others easier. If you're always struggling with not enough resources, but otherwise are doing fine, then a multiple planet start might fit your style well. If you tend to bottleneck so that the AI only has a few ways to attack you anyhow, then the other disadvantages of a multi planet start would start to fade quicker, too.
So it's really a personal preference sort of thing -- the game is different when you play with multiple homeworlds, and it just depends on what you find easier/harder and more or less fun.