I have the #3 pick in the draft and have 2 guys I'd be really happy with. First is a SS with 58 health and second is a catcher with 89 health. SS is the better player but is the lower health a big risk even if I'm planning on keeping 20 in medical for at least 2-3 more seasons? Ty for any responses.

I don’t care about health for position players unless it’s super low or I want to play them at 2B. Even at 2B I wouldn’t flinch at 61.

First off, Training budget helps avoid injury; Medical budget affects recovery.

Health affects a player's ability to avoid short-term injury. A player with Health lower than, say 50, will miss multiple parts of the season with 7,8,9-day injuries, that kind of thing.
However, ANY player can suffer ANY long-term injury. Even with 98 or 99 Health. The two most extreme cases I've had on my team are a hitter with 48 Health who never went on the 60-Day list during an almost-HOF career. But I had a pitcher with 82 Health need not one but TWO elbow surgeries.

When drafting players I use Health as a tiebreaker if I feel like it. A 90+ player is nice to have around if you want him playing every game. One of my best players right now has 60 Health and I always have to be ready that he might have a DL stint any and every season. With bad timing, maybe even while I'm fighting for a playoff spot. But that's random chance.

If you have 20 in medical the lower health may actually be a blessing. Its not as good as it used to be but you can still gain points by putting guys on the long term IR. The SS that you have may take a couple of 15-20 day injury stints like Damag said, unless you need him, you can put him on the 60 day IR and have him gain points in ratings where he otherwise may have reached a cap.

Yet sometimes it's just random.
Rip Bromberg 3B - 1st pick overall - 56 health - 9 ML seasons, has only played less than 160 games three times - two of them he still played 154 & 158.
Gregorio Cordero C - 1st pick overall - 50 health - 5 ML seasons, has had some minor injuries but still manages 150+ games outside of his sophomore season.
Douglas Laxton LF - 2nd pick overall - 56 health - 6 ML seasons, less than 150 games only once (lower durability so I lowered the expectations) - and yet it was still 144 games.
Mallez Borenstein CF - 8th overall pick - 55 health - 9 ML seasons, only two seasons below 158 games (151 & 133)
Dane Castilla 1B - 4th overall pick, 54 health - 11 ML seasons, less than 150 games twice (149 & 83).

Disregarding rookie seasons when they were called up after the season started. Not sure what the owners were running as medical, but random does what random does! I've seen 99 health have more regularly occurring injury problems than some guys in their 50s on the same team. Hope I didn't just jinx those owners, sorry guys!