Working as an employee for the company would probably be more︂ complex and more expensive, as the company would be probably paying you social security expenses︃ in HK, but I'm just guessing, I have no idea how this works, it depends︄ how HK regulate this.
Invoicing would be more simple, as it would be an expense︅ for the company and it would be taxed as is in spain. From what I︆ know in Spain you have to pay a "cuota de autonomo" which is reduced for︇ the first two years, and then you pay taxes based on your income, with some︈ deductions. So if you invoice 3k € each month you will pay taxes on 36k︉ € at the end of year in spain ( and 36k less taxes in HK︊ as they are expenses ) + the cuota ( as an autonomo you have to︋ pay the cuota even if you don't make money ). How to optimize taxes in︌ spain as an autonomo is something you can ask a Gestoria, it's something they should︍ know, or I have some contacts that have been given me by spanish friends, ping︎ me a DM if you need them. You also get the rights to a pension️ after 15 years. The good thing about being an autonomo is that you can boost (your earnings in case you need to, like to get a loan, and then go back lower the next year, which is something more complex to do as an employee.
If you go this way and keep any relationship with the HK company hidden, do make sure the swiss bank account of your company doesn't report you to spain as beneficiary owner, you should be ok, and also solve the issue of not paying taxes anywhere, which could get you in trouble in the long run.