This should be it

Removed special check for plants. Bees undo it all so it's not worth the trouble just yet.
Credit for Crazylemon for being best coder. He helped me find a lot of issues that I would have been too stupid to find myself. Runtimes are gone

code/game/data_huds.dm

@@ -323,26 +323,26 @@
 ~~~~~~~~~~~~~~~*/
 /proc/RoundPlantBar(value)
 	switch(value * 100)
-		if(91 to INFINITY)
-			return "max"
-		if(81 to 90)
-			return "90"
-		if(71 to 80)
-			return "80"
-		if(61 to 70)
-			return "70"
-		if(51 to 60)
-			return "60"
-		if(41 to 50)
-			return "50"
-		if(31 to 40)
-			return "40"
-		if(21 to 30)
-			return "30"
-		if(11 to 20)
-			return "20"
 		if(1 to 10)
 			return "10"
+		if(10 to 20)
+			return "20"
+		if(20 to 30)
+			return "30"
+		if(30 to 40)
+			return "40"
+		if(40 to 50)
+			return "50"
+		if(50 to 60)
+			return "60"
+		if(60 to 70)
+			return "70"
+		if(70 to 80)
+			return "80"
+		if(80 to 90)
+			return "90"
+		if(90 to INFINITY)
+			return "max"
 		else
 			return "zero"
 	return "zero"
@@ -357,16 +357,10 @@
 
 /obj/machinery/portable_atmospherics/hydroponics/proc/plant_hud_set_status()
 	var/image/holder = hud_list[PLANT_STATUS_HUD]
-	// Dis be drugs here. And special mention plants
-	var/list/special = list(/datum/seed/nettle, /datum/seed/apple/poison, /datum/seed/ambrosia, /datum/seed/tobacco, /datum/seed/mushroom, \
-							/datum/seed/weeds, /datum/seed/grass, /datum/seed/kudzu, /datum/seed/diona, /datum/seed/clown)
 	if (!seed)
 		holder.icon_state = ""
 		return
 	if (harvest)
-		if (is_type_in_list(seed, special))
-			holder.icon_state = "hudharvest2"
-			return
 		holder.icon_state = "hudharvest"
 		return
 	if (dead)

code/modules/hydroponics/trays/tray.dm

@@ -87,6 +87,17 @@
 /obj/machinery/portable_atmospherics/hydroponics/New()
 	..()
 
+	var/datum/atom_hud/data/hydroponic/hydro_hud = huds[DATA_HUD_HYDROPONIC]
+	prepare_huds()
+	hydro_hud.add_to_hud(src)
+	plant_hud_set_nutrient()
+	plant_hud_set_water()
+	plant_hud_set_status()
+	plant_hud_set_health()
+	plant_hud_set_toxin()
+	plant_hud_set_pest()
+	plant_hud_set_weed()
+
 	component_parts = list()
 	component_parts += new /obj/item/weapon/circuitboard/hydroponics(null)
 	component_parts += new /obj/item/weapon/stock_parts/matter_bin(null)
@@ -103,16 +114,6 @@
 	if(closed_system)
 		flags &= ~OPENCONTAINER
 
-	var/datum/atom_hud/data/hydroponic/hydro_hud = huds[DATA_HUD_HYDROPONIC]
-	prepare_huds()
-	hydro_hud.add_to_hud(src)
-	plant_hud_set_nutrient()
-	plant_hud_set_water()
-	plant_hud_set_status()
-	plant_hud_set_health()
-	plant_hud_set_toxin()
-	plant_hud_set_pest()
-	plant_hud_set_weed()
 
 /obj/machinery/portable_atmospherics/hydroponics/upgraded/New()
 	..()
@@ -175,6 +176,8 @@
 	pestlevel = 0
 	plant_hud_set_status()
 	plant_hud_set_health()
+	plant_hud_set_weed()
+	plant_hud_set_pest()
 
 //Harvests the product of a plant.
 /obj/machinery/portable_atmospherics/hydroponics/proc/harvest(var/mob/user)
@@ -618,6 +621,7 @@
 			user.visible_message("<span class='danger'>[user] starts uprooting the weeds.</span>", "<span class='danger'>You remove the weeds from the [src].</span>")
 			weedlevel = 0
 			update_icon()
+			plant_hud_set_weed()
 		else
 			to_chat(user, "<span class='danger'>This plot is completely devoid of weeds. It doesn't need uprooting.</span>")