What I've heard is that the modern 5Y3s don't drop enough voltage in a vintage amp that was designed for one, and so filter caps and other components may suffer undue stress or suddenly fail when a new replacement is fitted. I've also heard that Sovtek 5Y3s are basically "GZ34 rejects," because they don't meet the higher specs, but they still "work." So label them as something less... That said, I've never seen a Spvtek 5Y3, so I don't know what the innards look like to compare. Also that said, I have never had a rectifier tube in any of MY amps short or fail, regardless of what brand or date they were. I HAVE repaired several amps that suffered a blown rectifier, but they also had blown fuses and/or power tubes/filter caps.
When buying new, I use JJ. Of the 3 I've had, all work fine. As far as a substitute, they pretty much will all "work," but in the case of using a 5V4 in place of a 5Y3, watch out that your voltages don't rise and blow any other components, mainly filter caps. I'm now partial to 5R4s, myself - drops as much voltage as a 5Y3 but takes higher input voltages & output currents.