Sorry Karyn I mean will slow my PC down having lots of files is it better to keep them on a separate hard drive? 

A "standard" setup would be to have "load once" programs, like Sonar on the system drive along with Windows.
A second HDD for projects and audio files (I keep my plugins folders on it as well) and maybe a third for sound libraries like Kontact or BFD3 or SD1 Where you'll have many Gb of "load once" audio.
 
You can improve general performance by using an SSD for the system drive, but a standard 7200rpm HDD is fine for audio and library drives.
Increasing RAM (on a 64bit system) will reduce the amount of disk streaming from libraries.

At the moment I have all audio files & plug in folders & sound libraries on my PC hard drive if I move them all on an external hard drive if I move them all will it cause me hassle rescanning them? 

If you are using sample libraries consider a separate internal hd just for the samples. Samples are not completely loaded into RAM. Usually just the header is loaded and the rest is streamed from the hd.

You're better off with a second (or third) INTERNAL HDD, rather than external, that can be directly connected to ports on the motherboard.
 
When it comes to moving and re-scanning,  I know of no problems with your projects and audio folders, just tell Sonar where to look.  The same goes for Plugins and Libraries BUT some programs my need re-registering with Windows to work..  depends on the program.  I'm not the right expert here..  (or any expert... but don't tell anyone..)

I would not be concerned about file access/streaming at this point. Latency is essentially fixed by the drivers, firmware and hardware, and system performance/resource issues will manifest as pops/crackles/dropout, not added latency. And moving things to an external drive probably won't help performance, anyway, unless it's external SATA.
 
If the latency is project-specific, it's most likely due to a plugin that uses look-ahead buffers to process audio, and requires Plugin Delay Compensation, delaying other tracks to maintain sync. Common offenders are convolution reverbs and Cakewalk's own Transient Shaper and LP64 plugins. These plugins are meant for the mixing stage when latency is not a concern.

Thanx guys since iv been using sonar(since last November) iv never had a issue which this forum has not found solutions for... What a collective source of knowledge u r😉👍👍👍

Just a tip. I have a 2.5" SSD, and I got a 2 in1 adapter, and also attached a 1tb 7200rpm 2.5" drive from a  water damaged laptop. I may remove the 3.5" 1tb original drive, as it's pretty much sitting idle in there atm. I still have a 750(external) and 450(5400 rpm) both 2.5". So my point is, don't rule out 2.5" drives in a mid tower...

Is it best to remove all plug ins on the projects I am experiencing problems with? 
 

You can first try bypassing FX globally using the FX button in the Mix module (hotkey 'E'). If that does the trick, undo the global bypass, and start bypassing them one at a time in FX bins until you find the offender. There may be cases where the plugin has to be removed rather than just bypassed to eliminate the PDC.