Various claims have been made about this, mostly along the lines of "SRAM is cheaper" (and compared to flash RAM, it is).
But the most credible reference I've seen explains that of the options available at the time, SRAM was the least expensive one that could still fit save data for those games. EEPROM was less expensive, but had a much smaller space available for saving data for each game. Some games (those twelve, presumably) needed to save more data than could fit in an EEPROM, and so they had to use the more expensive SRAM option. Flash RAM was available as well and had even more storage than SRAM, but was also a lot more expensive than even that.
N64 developers basically had 5 options for save storage:
4kb EEPROM (512 bytes)
16kb EEPROM (2048 bytes)
256kb SRAM (32,768 bytes)
256kb SRAM Controller Pak (32,768 bytes) (some 3rd party Paks had even more memory)
1Mb FRAM (131,072 bytes)
EEPROM was the cheapest to produce but a lot of developers moved to SRAM because they needed more storage for their save files. Most developers went with SRAM over the battery-less and much greater capacity Flash memory because they were already forking over $30 or more on production costs alone for the N64 cartridge (deja vu with the Switch right now) and Flash memory was extremely more expensive back in the day. Only a small list of games actually used FRAM like Paper Mario and Pokemon Stadium 2 for example.