Nixson_security,
As I understand Throughput is reduced after configuring IDP or SSL proxy. Please refer the datasheet to check the performance numbers.
https://www.juniper.net/assets/us/en/local/pdf/datasheets/1000550-en.pdf
If you are not seeing the expected throughput what is described in datasheet then to start with you can look for below information.
First of all verify RE and PFE CPU, ensure this is not crossing threshold level.
show chassis routing-engine
show system process extensive
show security monitoring performance CPU
show log messages to see any idp related errors.
Also below kb link should help you with detailed steps of idp troubleshooting along with IDP configuration suggestions.
https://kb.juniper.net/InfoCenter/index?page=content&id=KB16561&actp=METADATA