Having all of those yes would be a nuisance, you're right. However, almost every article of clothing I take along on any given trip has a hood. I typically don't wear them all at once so interference or ill compatibility isn't usually an issue. I do find that the imperceptible amount of weight found in having a hood is worth every gram and ounce, as the ability to cut down on drafts and retain warmth to my upper body and head is much more effective with a hood, adding to the overall versatility and functionality of the piece in changing weather conditions and environs.
My windshell has a hood, but I don't typically pack my windshell and rainshell simultaneously on trips, so opted to having hoods on both. My preferred midlayer is very versatile, the BPL Beartooth Hoody has a balaclava style hood, it's very efficient, light, and warm for it's weight and the hood is a key feature in the piece. The BPL beartooth hoody hugs next to skin so it easily slides under and in conjunction with other hoods. My Montbell UL Down Parka also has a close fitting cinching hood, as this serves as my insulation piece for cold mornings and evenings. I chose the hooded option to serve in place of bringing an extra warm beanie or balaclava, again it's about versatility, weight savings, and function for me over a broader range of situations.
To answer your question more specifically, having a hood on your rainshell is to be expected and is ideal. The benefits of a hooded windshell also outweigh not having one in my opinion, but some choose to go with a simple hoodless version here (ex: Montane Featherlite Smock or Slipstream). Down jackets are one article of clothing that doesn't necessarily have to have a hood as well, it's very common to see hoodless down jackets.