It would not affect anything other than SMTP.
use Enable-ExchangeCertificate -Thumbprint JH3453987SKDFAHS2........ -Services "SMTP" ; restart transport service and you would be good.
The important thing to note is that you have Common name for the cert ( webmail.mycopanyname.com) = hostname of the box. else it won't work unless you have UC SAN certificate with hostname as an additional name in the cert.
Thx