According to an article by Media Village, Black Lightning's suit does indeed have a voice changer but I can't seem to track down a reference other than that so that might just be them making assumptions after watching the episodes.
However, it’s appearance and functionality in the actual show is much more solid. Cress Williams (pictured at top and above left) has got the TV superhero body type down, so there isn’t as much padding as I initially thought, and BL’s suit comes with a built-in voice changer, which alleviated some of my concerns about how people didn’t recognize their principal running around whupping ass at night with that tiny mask on.
Media Village, "Black Lightning": The CW's New Superhero Is Electrifying
On top of that Salim Akil, the director for Black Lightning, has said in some scenes they will be changing his voice, in this particular case a scene from the first episode where he is in front of his daughter. This would imply that they have at least thought about changing his voice to make him unrecognisable.
Why not give Jefferson a helmet to protect him from additional damage and also to keep his loved ones from recognizing him?
It’s an interesting line every time I read one of the scripts. I have a crew crew of writers, but I touch every script. And there was a scene recently in a script where Thunder and Black Lightning had on their suits, but they were in the house, and I was like, “Nah.” It varies from story to story and script to script, but I try to have rules I stick to — even if they’re still being set because the show is new.There’s a moment in the first episode where he’s literally right in front of his daughter, and he has the thing over the eyes, and we’re going to change his voice, but there’s not a lot more we can do, and you kind of have to just buy into it a little bit. I had a lot of iterations of his costume, and at one point I had covered his face and his eyes, but what was more important to me was the emotion, and you need to see that. You need to see his eyes when his daughters have a gun pointed at them.
Variety, ‘Black Lightning’ Boss on Telling a Tale of ‘African-American Paranoia’
However, none of that explains why he has a different voice when not in the suit, it wouldn't appear to be Jefferson putting on a different voice because it just doesn't sound right. My best guess is also backed up by someone on reddit who seems to think Jefferson is channelling lightning into his vocal chords to change his voice.
There are scenes where we see lightning channeling through his body while he's not in the suit. Best guess is that he's channeling that lightning to his vocal cords.
r/BlackLightning, How does BL change his voice for phone calls?, LinkinPlayground