Do secured and unsecured credit cards have a different effect on credit history/score?

Are there any differences between reports of secured and unsecured credit cards and their effect on my credit history/score?

No. The secured/unsecured status of your card is not reported to the bureaus.

If I upgrade my secured cards to unsecured, does it have any negative or positive effect on my history/score?

As the bureaus don't know if the card is secured, it cannot have an impact here. (Some lenders may up your limit when they unsecure the card, which will have a (positive) impact.)

Is it better to have one regular credit card plus two secured credit cards with $500 credit limit on each card or one regular credit card plus one secured credit card with $1000 of credit limit?

There are a number of factors here.

• Some lenders may base the highest limit they'll give you off the highest limit you already have. If they see you with a bunch of $500 credit lines, they may be unlikely to give you a $5k limit.
• Having less than three lines is considered a "thin" credit file, so there may be a benefit to having the third.
• In some scoring models, individual cards' utilization matters as well as your overall utilization. It may require more careful attention to your payments and statement dates if you're putting spend on the smaller limit cards and trying to manage utilization.

All this said, though, I'd generally advise not trying to micro-optimize like this. I'd pick cards based on lender reputation, rewards, and card features over the specific credit limit amounts you're looking at.