Re: payments - it depends on the country, but generally Stripe + PayPal + bank wires for larger/enterprise purchases. Alternatively, Braintree.
An altogether different option is to pay 2x the commission and use "full-service" reseller frontends like Digital River, PayProGlobal, etc. These are referred to as "registrators" and they used to be useful, because getting a merchant account and processing cards was a royal pain the ass. But now there's Stripe, so virtually no value in them. In fact, they tend to make thing more difficult to the clients than needed to justify their own existence (like requiring phone numbers, calling customers back to "verify" purchases and other artificial b/s like that).
Re: piracy protection - wildly depends on whom you ask. There is a camp of people that put minimum effort (literally a a single "if" check in the code) and embrace having their stuff cracked and hacked. The logic is that this acts as extra marketing and helps converting pirates (lol). There are also people who use packaged solutions like VMprotect and (previously) Armadillo. This tends to nip piracy in a bud, but creates issues with antivirus false positives. It also makes the software heavier and more fragile. There's also a middle ground of custom protection schemes that, if deployed wisely, can create 100x more headaches to crackers vs the effort spent on coding them in. Not that hard to do, but these aren't drop-ins, obviously.
Also, closely related, is the question of how the licensing works. Previously, most of the shareware used completely offline licensing using "keys" that were either hardcoded into the program or verified algorithmically (read, with elaborate checksums and such). This caused an emergence of keygens and it also fed credit card fraud with people smash-n-grabbing keys in bulk and then published them for the street cred. Surprisingly, a lot of shareware still uses this method and they still bitch and moan about the consequences. The alternative, obviously, is to use online activation. That is, what is sold is an activation token that can be swapped for a machine-specific license, via an exchange with the licensing server. This nearly completely eliminates the CC fraud and it allows for finer control over licensing. There are some drop-in solutions for this, but all of them are really quite basic and almost universally suck. However, the good news is that is fairly simple to roll out your own online licensing scheme in a matter of few work-days (assuming you know a bit of web backend and frontend).