I have had to grapple with the same issue for a while, but only because I started removing fonts from the System > Library > Fonts and the Library > Fonts folders. I even had Axure Pro crash on opening files because of missing fonts. I decided to spend some time testing which fonts are causing the issues if missing (removed). I did a "restore" of OSX by restarting a test drive and using "Command+R" to go into restore/ utilities, terminal mode at startup. 30 min of restoring later all the fonts came back. OSX El Capitan installs over 1 GB of fonts between the System > Library > Fonts and the Library > Fonts folders ⚠.
I started removing some fonts from both folders just for the sake of it and test the system. I could usually test quickly between iMessage and emojis in messages if a required font was missing. I also looked at other apps and font displays. I managed to cut fonts down in these two folders to about half of what OSX installs by default.
Hopefully this will help. Here's a list of fonts I have between the System > Library > Fonts and the Library > Fonts folders and everything on my Mac is hunky dory (I'm not saying these are all required, I'm sure I could cut the list down more but I haven't had time to play with it more):
System > Library > Fonts:
Apple Braille Outline 6 Dot.ttf
Apple Braille Outline 8 Dot.ttf
Apple Braille Pinpoint 6 Dot.ttf
Apple Braille Pinpoint 8 Dot.ttf
Apple Braille.ttf
Apple Color Emoji.ttf
Apple Symbols.ttc
AppleSDGothicNeo.ttc
AquaKana.ttc
ArialHB.ttc
Avenir Next Condensed.ttc
Avenir Next.ttc
Avenir.ttc
Courier.dfont
Geneva.dfont
HelveLTMM
Helvetica.dfont
HelveticaNeue.dfont
HelveticaNeueDeskInterface.ttc
Hiragino Sans GB W3.ttc
Hiragino Sans GB W6.ttc
Keyboard.ttf
LastResort.ttf
LucidaGrande.ttc
Monaco.dfont
Noteworthy.ttc
PingFang.ttc
SFNSDisplay-Black.otf
SFNSDisplay-Bold.otf
SFNSDisplay-Heavy.otf
SFNSDisplay-Light.otf
SFNSDisplay-Medium.otf
SFNSDisplay-Regular.otf
SFNSDisplay-Semibold.otf
SFNSDisplay-Thin.otf
SFNSDisplay-Ultralight.otf
SFNSText-Bold.otf
SFNSText-BoldG1.otf
SFNSText-BoldG2.otf
SFNSText-BoldG3.otf
SFNSText-BoldItalic.otf
SFNSText-BoldItalicG1.otf
SFNSText-BoldItalicG2.otf
SFNSText-BoldItalicG3.otf
SFNSText-Heavy.otf
SFNSText-HeavyItalic.otf
SFNSText-Light.otf
SFNSText-LightItalic.otf
SFNSText-Medium.otf
SFNSText-MediumItalic.otf
SFNSText-Regular.otf
SFNSText-RegularG1.otf
SFNSText-RegularG2.otf
SFNSText-RegularG3.otf
SFNSText-RegularItalic.otf
SFNSText-RegularItalicG1.otf
SFNSText-RegularItalicG2.otf
SFNSText-RegularItalicG3.otf
SFNSText-Semibold.otf
SFNSText-SemiboldItalic.otf
Symbol.ttf
Times.dfont
TimesLTMM
ZapfDingbats.ttf
ヒラギノ明朝 ProN W3.ttc
ヒラギノ明朝 ProN W6.ttc
ヒラギノ角ゴシック W0.ttc
ヒラギノ角ゴシック W1.ttc
ヒラギノ角ゴシック W2.ttc
ヒラギノ角ゴシック W3.ttc
ヒラギノ角ゴシック W4.ttc
ヒラギノ角ゴシック W5.ttc
ヒラギノ角ゴシック W6.ttc
ヒラギノ角ゴシック W7.ttc
ヒラギノ角ゴシック W8.ttc
ヒラギノ角ゴシック W9.ttc
Library > Fonts
Andale Mono.ttf
Apple Chancery.ttf
AppleGothic.ttf
Arial Bold Italic.ttf
Arial Bold.ttf
Arial Italic.ttf
Arial Unicode.ttf
Arial.ttf
Calibri Bold Italic.ttf
Calibri Bold.ttf
Calibri Italic.ttf
Calibri.ttf
Chalkboard.ttc
ChalkboardSE.ttc
Courier New Bold Italic.ttf
Courier New Bold.ttf
Courier New Italic.ttf
Courier New.ttf
Georgia Bold Italic.ttf
Georgia Bold.ttf
Georgia Italic.ttf
Georgia.ttf
GillSans.ttc
Lucida Sans
Lucida Sans Unicode.ttf
Microsoft Sans Serif.ttf
MS Reference Sans Serif.ttf
MT Extra
News Gothic MT
NISC18030.ttf
STIXGeneral.otf
STIXGeneralBol.otf
STIXGeneralBolIta.otf
STIXGeneralItalic.otf
STIXIntDBol.otf
STIXIntDReg.otf
STIXIntSmBol.otf
STIXIntSmReg.otf
STIXIntUpBol.otf
STIXIntUpDBol.otf
STIXIntUpDReg.otf
STIXIntUpReg.otf
STIXIntUpSmBol.otf
STIXIntUpSmReg.otf
STIXNonUni.otf
STIXNonUniBol.otf
STIXNonUniBolIta.otf
STIXNonUniIta.otf
STIXSizFiveSymReg.otf
STIXSizFourSymBol.otf
STIXSizFourSymReg.otf
STIXSizOneSymBol.otf
STIXSizOneSymReg.otf
STIXSizThreeSymBol.otf
STIXSizThreeSymReg.otf
STIXSizTwoSymBol.otf
STIXSizTwoSymReg.otf
STIXVar.otf
STIXVarBol.otf
Tahoma Bold.ttf
Tahoma.ttf
Times New Roman Bold Italic.ttf
Times New Roman Bold.ttf
Times New Roman Italic.ttf
Times New Roman.ttf
Trebuchet MS Bold Italic.ttf
Trebuchet MS Bold.ttf
Trebuchet MS Italic.ttf
Trebuchet MS.ttf
Verdana Bold Italic.ttf
Verdana Bold.ttf
Verdana Italic.ttf
Verdana.ttf
Webdings.ttf
Wingdings 2.ttf
Wingdings 3.ttf
Wingdings.ttf
Zapfino.ttf