Is there a way to clean up the Hikashop product database?

Hi,

3600*~10 variants is only less than 50 000 entries in the hikashop_product.
That's not what is eating your database memory. It shouldn't take more than a few MB. Normally, variants don't have a description and just use the description of their main product, and the description is the main thing eating the memory for a product entry.

The first thing to do is to open your PHPMyAdmin and check the number of entries for each table in the database and the size of each table. I would wager the problem is elsewhere, in another table.
For example, if you've been running HikaShop for years with the Email history plugin activated without a "number of days" set in its settings, the email log table in the database has been steadily growing without any cleanup of its data. The emails take quite a bit of space individually, so if you have hundreds of thousands of them, that could take a significant share of the pie.
It's been a while now that this setting has been added with it's default set to 30 days. But if you updated from an old version, it's possible that you still have that setting empty.

But it could be something else entirely. I'm just talking about the email history because that's something that happened to someone else in the past. Anyways, what to do next depends on what you find in the database.