What on earth are they using for their database that means they are running into space issues? Databases are designed to scale to hundreds of thousands (if not millions) of records so long as you have sufficient storage space...
Overall, they are not using anything that quite resembles to any traditional type of database. Talking from PC perspective, where almost everything is moddable.
What is colloquially called "database" in PES is actually a bunch of internal .bin files within large .cpk containers. Those .bin files
are fundamentally not limited at all - e.g. fundamentally, you can add as many new player blocks into Player.bin and create unlimited supply of players. Same goes for teams in Team.bin file, for team rosters in PlayerAssigmnent.bin, etc. Each individual data block (be it player, team, ball, face, boot, glove, ...) has its unique ID (just like in traditional databases) and data blocks are linked across various .bin files using those IDs - e.g. Player X belongs to Team Y, etc. Just like in traditional databases.
So, that layer of storage actually resembles to traditional database and it could support huge amount of players and teams. The only real limit should be the length of those IDs ... but since (almost) all of them are 4-byte long (32 bits), they allow for up to 4,2 billion (4,2 thousand millions) of unique IDs ... 4,2 billion players, 4,2 billion teams ... purely theoretical limits in term of an actual gaming content.
That being said, Konami has imposed several internal .bin file limits of their own, to be able to handle duplicated players in Master league (duplicates such as e.g. licensed Modrić in Real Madrid vs unlicensed Modrić (Mognac) in Croatian NT, so that they wouldn't appear both in the market) and special versions of certain teams (frozen-in-time versions of ACL, Libertadores and/or Sudamericana teams). So, more practical limits, due to those quite archaic internal rules are that we have ~200000 usable player IDs and ~16000 team IDs. Still quite a lot and more than enough to sustain all those newly obtained leagues and players.
The real show-stopper is the second part of the data storage, which hasn't changed much in 2 decades - an incredibly rigid and 100% fixed-sized EDIT00000000 file (i.e. option file). This file is used as a mash-up that contains copy of everything that is editable in game (players, teams, rosters, ...). Sadly, that storage has virtually 0 scalability ... Konami sets the hard-limits every year and those limits cannot be surpassed. And those limits are really low. Yes, there's always some additional space inside for new players and teams, but those limits are ridiculously small compared to the internal .bin files.
@falcom4ever had mentioned 150 teams limit for PES 2018 ... while internal .bin files could merrily support 1500 new teams, external EDIT file does not have enough pre-allocated empty space to contain 1500 teams, it can barely contain 150 new teams. Add more than allowed hard-limit and you'll start overwriting data from another section in EDIT file ... thus, turning it into corrupted garbage.
And the cherry on top - EDIT file is only 5 MB in size. Why??? They don't make PES for PS3 or PS2 any more, right? Why don't they finally liberate the EDIT file from those ancient PS2-shackles? What console that PES is made for would have problems with EDIT file having 50 or 100 MB in size?