dedicated server cannot handle the database query?

[w2e]

how do i confirm/check?
If that is the case, how do i restore the indexes?

[DrByte]

how do i confirm/check?

You can see the indexes via phpMyAdmin when looking at each table's structure.
Or you can export structures and compare against the original Zen Cart files.
Or you can hire a professional who handles this sort of thing all the time.

If that is the case, how do i restore the indexes?

You'll have to manually build them all based on the original Zen Cart structure, or again, hire a professional who is familiar with the process.

[w2e]

update:

We have since moved the site from inmotionhosting to another, and after 1 month, we are now running our own dedicated server.

The conclusion is that the problem is not about if zen cart can handle how many items. The problem is about the hosts! All the hosting companies want is money from you - the more the better! different companies use different tactics.

The highest item count on our site so far is over 103K without a problem. The google webaster tools show our load speed at 0.7 - higher than 93% of the sites. All this has been done without making any changes to zen cart.