It's cheaper and possibly more reliable than providing a connector. These are disposable consumer products designed to be sold at the lowest price and highest margin.
Your question assumes devices like the N64 Controller Pak are designed to be user serviceable - they're not. Take a look at the N64 Controller Pak manual: the instructions are little more than how to remove and insert it and a warning not to mess with it. The majority of video game accessories and games, especially ones with lithium coin cell batteries are not meant to be user serviceable. The list includes Game Boy and Super NES Game Paks; Master System, Mega Drive and Game Gear cartridges; and Nintendo 64 Games and Controller Paks.
If they're damaged or develop a defect, the manufacturer's intended remedy is that you send it to them for a repair, preferably outside of warranty so you have to pay them. They're engineered to function well enough during their active supported profitable lifetime, and that's it.
Conversely, there are some console memory cards that do have replaceable cells, like the Dreamcast VMU, however the purpose of that is to let players use the VMU in detached form as a game system, and also for save game management and copying (this is why the VMU has a symmetrical connector). VMUs were expensive.