I tie & use a lot of weighted flies, some very heavily weighted. I still use lead wire, barbell eyes, beads & cones of the various materials. They all sink differently.
But, I've never given that a lot of though either. None are ever weighted so much I can't cast them. In shallow water, if I'm using a weighted fly it's usually going to be fished on the bottom, So I just count down until my line goes slack. In deeper water, I'm usually using a sinking line, of which I know the sink rate, and again just count down to whatever depth I'm trying to achieve. The flies hardly ever sink faster than the line. I'm also primarily fishing in tidal rivers which often have strong currents. The same fly will sink at different rates because of the current, and since tidal currents fluctuate so much, knowing the sink rate of the fly in still water is of little value. I just make my adjustments in the field.
I've also been tying a long time, and pretty much use the same amounts of weight on a given size hook, so have a good idea how fast they sink. It's just one of those things you do so much there's very little extra thought needed.
As far as using lead, it's the oxide of lead that causes problems. Pure elemental lead is not soluble in water, but the oxide & other compounds certainly are.
When I use wire, I seal it with a coat of cement, not so much because of health concerns, but because I don't want it oxidizing within the fly & discoloring it. If I lose a fly weighted with lead, in the places I fish most, I feel that once it settles into the mud bottom, and is covered with slit, where there's likely not much O2, IMO it's not going to cause any problems, at least no more than what's probably already there, particularly the small amounts used in flies. However, if you feel it's not something you want to use then don't.
I have started to get away from using lead barbells, but only because I've had them break too often. I tie more with brass now. Tungsten would be better, but normally too costly, unless I can get them on sale!