EP (employment pass) Malaysia

this is allowed quota for each company to hire foreigners from overseas. they only give this on the basis of eligibility of company to hire such number of foreigners in category 2 or 3

This process is what MDEC called Foreign Knowledge Worker Projection ( quota application ). Mdec is very efficient with this as long as companies provide all required documents. Mdec usually takes 1-2 days to reply to companies if the documents is sufficient ans it is up to the companies to furnish all pending documents. Hope this clarifies!

before your company could apply for your employment pass/visa, they need to have an approved slot - which is the  approved quota to hire foreign workers. since your company has not been given yet the slots, they haven't applied for your work permit, hence you can't check it

I'm thinking it is because Expat Services has been closed for a few months now due to MCO. My working permit was renewed first week of June and until now application is pending stage 2 (endorsement). According to agent, queues in Expat Service center were all removed on the onset of EMCO and so companies/agents will need to queue again after it opens, which I don't know when.

All above are correct  and EPs are now 10x harder to get, especially in areas where the government deem there are locals who need jobs.

Realistically you need a Plan B assuming you wont get an EP soon, you might still get one but the signs are not good. Plan B probably involves going back to your home country and findingal a  job. If I was you I would start job hunting now back home.