Because all of the hacking tools were made for those specific games(including Ruby), and as sumwun says, the most usable and "popular" tools make Emerald and Fire Red super easy to hack. There are also new features that have been developed for only Emerald and Fire Red like the Gen 7 Battle Engine for Emerald, the JPAN hacked battle engine for Fire Red, and the MrDollSteak patch for Fire Red.
Tl;Dr
They're easier to hack because of all the tools that support them
Source: I'm a ROM Hacker myself