In the games that I referee (SCDSL, ECNL, etc.) that have restrictions on substitutions, the referee crew tracks the substitutions. It is easy to track the substitutions if the referee crew requires the player to completely leave the field of play before the new player can come on. SCDSL, ECNL and DA all allow the referee to add time at the end of each half, so there is no reason why referee crew would not be able to track the substitutes. I know that not all referees track the subs in these leagues, because I have had coaches try to put players back in the game after they have been subbed out. When I tell them that their player cannot reenter for the half, their response is usually, "The other referees let us do it." And, my response is usually, "Evidently they did not read the (SCDSL, ECNL, etc.) rules."
A few years back we had a S-20 team playing in USL. That league allowed every player to enter once per half. The league setup was both teams on the same side of the field, with a scorer's table at center line on that side. On that table were placed the game record sheets and the player cards. The referees that knew what they were doing took the player cards from each player as they entered the half, including at the start of each half. Once they had a player's card, he could sub out, but he wasn't getting back in.