After recently learning that it has a battery inside of it, I unscrewed my Controller Pak (N64 memory card) to put in a new battery. The old one says "98" on it, referring to 1998. So it's likely running out of power.
The battery is soldered on.
Why do this for something which will inevitably run out of power and need to be replaced? I thought it was just going to be a normal battery swap like so many other things using those flat, round batteries.
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.
Replacing the battery wipes the memory card, losing all your savegames.
Note that if you had a battery clip, there is a potential risk that the battery terminals might become oxidised or be jolted loose by vibration, which would also result in losing all your savegames. Evidently they took the choice to give you a decade of reliability in exchange for having to replace the whole thing at the end.
This was not an uncommon practice - many PCs of the era had soldered on motherboard SRAM retention batteries.
I doubt you'll find any actual reference here but things that look to be silly from an engineering viewpoint often make more sense from a financial one. N64 memory cards are mass-market consumer products and generally cost is a significant consideration in the design and construction. Leaving out a battery holder saved a tiny amount but in total likely summed up to a large figure.
They probably considered the "lifetime" of the card to be "X" years and as long as it continued to work for that long, the company was happy and customers were unaware of the "ticking time bomb".
Ok, so now you're a long way down the road and trying to use one of these cards that Nintendo considers obsolete. What do you do? You can solder a new battery in place and keep going or you can do what Nintendo wants and scrap the thing and buy a new "modern" Nintendo system.
The N64 has an interesting design choice that influences the way the peripherals were designed. Memory cards were attached to the controller, not the console. This means that during normal use, a memory card would experience significantly more movement than would, say, a console-attached Playstation memory card (which would remain stationary for most of its life). When you fall off rainbow road one too many times and toss the controller on the floor in frustration, that memory card gets jarred around and a socketed battery could come out of its socket and your saved data goes *poof*. Soldering the battery in place is a quick and cheap way to ruggedize the design.
I had a third-party "rumble pak" clone that included a pass-through connector where a memory card could attach. The memory card that came with it used a battery socket, but the battery was soldered into the socket. From all appearances, it was initially designed to be replaceable but later changed after testing. After all, every time the controller rumbled, it would be slinging the memory card around. That sort of constant vibration is certainly enough to gradually loosen the spring clips that hold the battery in the socket until the connection becomes unreliable. Ruggedized battery holders exist, but space is limited and solder is easier.
This wasn't a new problem for Nintendo. They had years of experience producing Game Boy games that included battery-backed memory, which would see the same sort of forces applied to them during use (I can't tell you how many times I violently shook my Game Boy in frustration). They had already learned that soldering the battery led to more reliable results. In fact, the retention mechanism used in Game Boy games looks almost identical to the one used in Nintendo-branded N64 memory cards.
