Novotna wasnt that good. Graf is possibly the female GOAT. One shouldnt have expected her to do better than she did vs Graf. Mandlikova is about twice the player Jana is and she barely did better vs Navratilova and Evert than Jana did vs Graf. Jana was only a real contender on grass and maybe to a lesser degre carpet. She was never remotedly a contender for big titles on hard courts and clay. Thus the only surfaces you should expect her to challenge Graf at all or grass and to a lesser degree carpet, and looking at their history she did do that. So in an era with a 1 month grass season, with only 1 event most players play, you shouldnt expect anymore from Jana than she managed. We can say Jana should have won the 93 Wimbledon final, but Jana shouldnt have ever beaten Graf at the 91 Australian on super slow and bouncy hard courts, that was the mother of all flukes (rebound age is probably Grafs worst surface too, but she is amazing on any surface, while it is Janas worst surface by a long ways, she is even much better on clay), so the overall H2H is probably still exactly as it should be.
Even at Janas peak in 97-98 with literally a nothing field that was one of the worst in history, especialy in 97 and early 98, people didnt talk about the possability of Jana winning the Australian, French, and U.S Opens, despite that there was literally nobody but Hingis who could (other than possibly a couple others for the French only). At the 97 U.S Open there was literally no contenders besides Hingis, maybe a really fat and out of shape Seles, and a really fat and before her prime years Davenport, and that was it, and Jana despite being in her career best form and ranked number 2 much of the year and on her 2nd best slam surface after Graf, was laughed off by people as a possible winner as if it were a joke. Someone like Sabatini who gave Graf more trouble was a much better player than Jana Novotna, despite that both won only 1 slam, and also had the good fortune to have her 91-early 92 peak coincide with Grafs own slump, which greatly aided her overall H2H (Sabatini won only 4 of their 32 matches outside this good chance Sabatini peaking and Graf crashing 8 match swing). Someone like Martinez isnt much worse than Novotna and was hopeless vs Graf, granted a totally different playing style.
As for referencing Navratilova they might have similar playing styles but Navratilova is in a different planet to Novotna in everyway essentialy. Navratilova even way past her prime and in her mid to late 30s was 7-1 vs a prime Novotna, and gave her a bagel and breadstick in their last ever match aged 37. The two women are on a different planet in ability. Furthermore they dont even play that similarily, Novotna is more of an all court player who stays back alot, while Navratilova is more a pure all out serve and volleyer and chip and charger who persistently attacks the net at each opportunity. A few players, Monica Seles being one, actually had more trouble with Janas more unpredictable playing style in that sense, but Graf is more bothered by someone who is in her face coming in at all moments and Jana did not do that, she bided her time and picked her spots.
As for the Navratilova vs Graf matchup they played 10 of their 18 matches (aka more than half) during Navratilovas consensus prime from 82-87 (all from 85-87 mind you) and before Grafs consensus prime of 88-96, only 3 matches on slower courts, and Graf still tied 9-9, leads in slam finals 4-2, and trails in slams 4-5, so I would say Graf atleast held equal in that matchup. I actually think Navratilova was in her prime until 1989 which would make the H2H even worse from an analytical standpoint for Martina, but I know most that feel that way so I digress. The idea Navratilova was past her prime playing a prime Graf in all or even most of their matches is a myth. Alot of the myth comes from Martina playing until 1994 when she was in her late 30s, but she and Graf played only 4 matches the last 5 years of Navratilovas career. That and people forgetting that Navratilova was a late bloomer. Navratilova in 1987 and 1988 was the same age Serena was this year making fools of Sharapova and Azarenka, and something she is likely to continue doing until she retires, and already at that point a 17 or 18 year old Graf was beating her in various slam finals, beating her 6-3, 6-2 in Miami, beating her 6-2, 6-2 in Berlin on clay (actually that was in 86), beating her the last 2 sets of Wimbledon 6-2, 6-1, so doesnt sound like such a super tough matchup to me.
I wouldnt say Navratilova did well vs Graf since she was a bad matchup, but since she is arguably the female GOAT and such a great player. There is no indication serve and volleyers were a bad matchup for Graf, atleast not ones with limited power and alot of finesse and variety like Novotna. Natalie Tauziat is probably the player on tour most similar to Novotna, she is a bit of a poor mans Novotna, and she is 0-20 vs Graf, and didnt even win a set. DeSwaardt despite being a much lesser player overall, and Navratilova, both have alot more power in their games, hence why they gave Graf more trouble than Jana could. McNeil is the one and only mystery in this as she also didnt have much power and while she was 2-11 vs Graf I believe, did surprisingly well and was surprisingly competitive still for a player of her generally low rank and stature in the game. McNeil when she was on though had a bit harder serve and forehand than Jana Novotna (note I did not say better overall, just harder) and a much harder serve and forehand than Natalie Tauziat.