Thanks for your query.Based on the facts that you have posted you have Haematospermia mostly due infection in Seminal Vesicle
.You need to get few more investigations like
Scanning with Rectal Probe
2) Semen Culture and sensitivity.
3) Microscopic examination of Semen for A.F.B
As regards presence of Epididymal Cyst
consult qualified surgeon for clinical examination and advice.
There is no harm in ejaculating.