Formatting ggplot2 legend text in rows with "empty" slots

If it's fine for your to get rid of the legend key background then one option would be

1. to set ncols=3 in guide_legend
2. to add two additional categories to your factor to add two additional slots or keys to the legend
3. set the labels for these categories to an empty string and the color equal to the plot background color
4. additionally we have to set drop=FALSE to scale_color_manual so that these unused categories don't get dropped

library(ggplot2)
library(dplyr)

df <- df %>%
  mutate(supplement = factor(supplement,
                             levels = c("Control", "foo", "bar",
                                        "0.5 mM NA", "5 mM NA", "10 mM NA",
                                        "0.5 mM NI", "5 mM NAI", "10 mM NI")))

ggplot(df, aes(x = axis1, y = axis2)) +
  geom_point(aes(color = supplement), size = 4) +
  labs(y = "Axis 2", x = "Axis 1") +
  scale_colour_manual(name = "",
                      breaks = c("Control", "foo", "bar",
                                 "0.5 mM NA", "5 mM NA", "10 mM NA",
                                 "0.5 mM NI", "5 mM NAI", "10 mM NI"),
                      labels = c("No Treatment", "", "",
                                 "0.5 mM Nitrate", "5 mM Nitrate", "10 mM Nitrate",
                                 "0.5 mM Nitrite", "5 mM Nitrite", "10 mM Nitrite"),
                      values =  c("#003F5C", "white", "white",
                                  "#824ED4", "#31B3F7", "#FFA600",
                                  "#ABF13D", "#DC267F", "#16F5E3"),
                      drop = FALSE) +
  guides(color = guide_legend(order = 1, ncol = 3, byrow = TRUE)) +
  theme(legend.title = element_blank(),
        legend.text = element_text(size = unit(14, "pt")),
        legend.position = "bottom",
        legend.box = "vertical",
        legend.key = element_rect(fill = NA), 
        axis.title = element_text(size = unit(16, "pt")),
        axis.text = element_text(size = unit(14, "pt")),
        legend.key.size = unit(25, "pt"),
        legend.key.width = unit(0, 'mm'))