Could having LARGE amount of small files on your HDD Slow down the pc ?

I googled that but kinda couldnt find the answer i am searching for ...

Basically i am holding on to about 3 million pictures with questionable content due to server failure of a site with a questionable content i help moderate .
Problem is my pc feels just slow last couple days and im not sure if thats the cause of it .
Its about 800 gbs of Manga and Doujins ... first it was 600 then i got another 200gb batch sent over few days ago.

Thing is the PC was fine until maybe 2 days ago ( cant rly tell cause i havent use it past few days cause work and stuff ) ... but right now everything takes what it feels like far to long to load ...
Deleting a folder with 50 files thats less then a MB in size takes about 15 seconds , trying to open any of the folders with the manga that i havent opened before takes about 10 to 15 sec aswell .
If i had opened it before it seems to load in 2-3 sec , but first time open is just far to long it feels like .

So yeah wall of text aside , Could it be that having Ridiculous amount of small files on the Only HDD ( which is not even cut on different label drives ) slow down the PC ?

PS: Tried to run malwarebytes already ... it didnt catch anything so i dont think its a virus , but it can be i guess ... ?

Will add giveaways later on ... so check the topic again if thats what you came for

Edit: Thanks to everyone who helped me out , i think i got the general idea of what went wrong and how to fix it ... In the process of moving them to an external HDD Right now and then will preform the Cleanups Defragments and all the other necessary stuff ( but that will be after i wake up )

Feel free to join the giveaways in the first comment , nothing major sadly :|

Edit 2: Problem solved ... got rid of the ... um stuff ... dont question it >.>
Ran a defragment and everything is working fine now .
Thanks to everyone who helped me :)