Well, we also used to stone people, and some people profited a lot by having slaves do all the work, so I guess now I should be annoyed that somebody kicked the ladder under me 
It’s the scale issue. Alts are way to strong force multipliers. Like look at PI stuff, say you are smaller corp and you want to start SRP program and build stockpiles. Assume there is 2 corps, each one has 10 real people. One of the corp is using alts, another isn’t.
The one using alts can generate 30 toons pulling PI stuff from planets, generate far bigger profits and support their corp way better. They can also use their alts parked in space with OCR running software to be used as early warning system while they do something else, they can also build in parallel 10 carriers while enemy can build 3 of them in parallel. You done for the day, well, just log of your main and leave a cloaky alt somewhere to mess with enemy (without any risk or time sink to travel to the enemy systems). And to run those alts doesn’t cost that much more.
Even if you run them on different account, you parallelize your work to pretty much earn at same rate for one or ten accounts, then just keep reaping the 10 time the profits. For example, if one miner takes 3 days to earn his plex, if you send 10 of them in the field, you will need maybe 4 days to earn plex for each of them, but every day after that it is 10 times more the yield, that is how we ended up with all the supers in game.
Back in the day they were rarer, not because of some magic new feature, but because people would at most have 1 alt. These days everybody needs to have multiple accounts to be competitive, this is what I see as problem. Where it took corp effort or really long time to make a super, now you have 5 guys with 10 alts each who keep churning them. You have 5 guys with 10 rorquals each providing materiels. CCP is combating this with introduced scarcity, but again, this is easy to combat with alts. You lost some minerals in null? well, start few highsec mining alts and then just jump it in a freighter…
Overall, the biggest issue is scaling in bigger entities, the bigger the corp / alliance, the greater the effect of everybody running alts. Every problem can be solved more easily with alts, without it being that much more expensive in the long run, hence the issue. I always found it strange that EVE allowed for multiple clients comparing to other online games, it just made little sense on balancing side.
Ofc it is hard to ignore the profits from CCP side, but this narrative that asset accumulation needs to be combated, that there is to much isk in game, to much capitals, etc, all can be boiled down that most of these issues are there since the force multiplier of alts. From EVE uni, apparently hulk can be filled in 5 minutes, for one player it would mean 12 loads per hour, assume EVE is your second job and you do 8 hours per day. That is 96 loads per day, 2880 loads per month for one person.
In comes alliance / corp with alts, lets say 4 miners per person is more than manageable, you have either highsec, or your warning systems, etc… Now each person is pulling 11520 loads per month. According to some reddit post, you need 60 hours of mining with Hulk to earn for plex. So in this example, one person with one account makes 240 hours per month, earns for 4 plexes, uses 1 plex and has 3 plex worth of profit. One person with 4 accounts mines effectively 960 hours per month, earns 16 plexes, uses 4 plexes, has 12 plex worth of profit, but they both invested the same time overall doing same activity, multiboxer just clicked 4 times for each one click of real player.
Ofc sooner or later everybody and their mother will be in titan and we will use DD’s only to kill each other, ofc no matter how many quantum core features you make, structure spam will just continue, no matter how much resources you redistribute, alts fleets will just adapt…
So to sum it up. Are alts bad design for game - sure they are. Are people wrong for using them? Well, no, why not use every edge you can, but at least realize that it in long term affects game very very much, some will argue for better, some for worse, but nevertheless, the effect is going to be even more harder to ignore in future.