For typical aerospace structure joints:
for metallic structure, see
Bruhn, Analysis and Design of Flight Vehicle Structures
Peery, Aircraft Structures (1st edition is better)
Niu, Airframe Stress Analysis
for composite structures, see
ASM Handbook, Volume 21 Composites (
Niu, Composite Aircraft Structures
I'm not aware of a specific bolted joint text, and most composite structure joint analysis method are company proprietary.