Rare Balls are like (Love Ball), (Moon Ball), (Friend Ball), etc. only available in HGSS.
Safari Ball imported all the way from RSE.
(Dream Ball) w/ HA from Gen V, now unavailable due to Dream World being discontinued.
Importing from RSE and HGSS is tedious and thus, the balls are rare because not a lot of people can do it. You need Bank for sure, and not everyone has Bank. You also need a copy of BW/B2W2 completed post-game as well as HGSS and a copy of XY. Again, with Bank, and it has to be a female Pokemon to work.
Plus, Kurt's timing to create PokeBalls can be rather icky.
Safari Balls are even rarer as you need to import to HGSS from RSE (requires a DS Lite or normal DS), then HGSS->completed copy of B2W2/BW + Pokemon Bank.
(Dream Ball) females with HA are even rarer now that importing is impossible. You can no longer catch them because of Dream World discontinuation.
Female Pokemon in Rare Balls are more valuable than Pokemon in normal, Gen VI balls with the same EMs, IVs, etc. because of rarity. It's just extra effort and people like it. That's how I completed my DEX easy. I had traded for so many Rare Balls in the past, and Cyclone is recently getting a bunch for me and importing (more exclusive balls this way; wee~), and it's really enticing for people to trade for in exchange for regular Pokemon DEX fillers.