1. HM2's autorate icons are not always reliable. Some argue they're deceptive and should be eliminated, which is the approach taken with PT4. That said, the rules that create them are customizable and are based on pure stat filters and sample sizes. I don't remember the exact Whale rule offhand (at work and don't have HM2 in front of me) but as I recall it's generally a huge VPIP, minimal RFI/PFR, either low AF or high WTSD. I will say if it still flags someone as a whale after a couple hundred hands, then they probably are. As to whales with stacks, nothing about stack sizes or winnings factor into the autorate icon AFAIK, it's based strictly on how they play. You should know that terrible players can luckbox themselves into big stacks from time to time, but it's a high variance thing -- they will spike far more bustouts and losses over the long term.
2. Haven't looked at LeakBuster in years, since I played 50NL at pretty high volume, but it was pretty good back then if you knew how to filter and use it properly. I'm sure it's probably improved since then, I own it but haven't played cash to speak of for a few years now so haven't kept up with the latest updates.
3. Answered. Both HM2 and PT4 offer upgrades to their Pro versions that roughly equal what you would have paid outright for Pro. If you're a long way yet from moving across their stakes threshold, there's not a lot of reason to invest in the Pro version right away.