You will need to convert the time aspect into a time only column then filter out where >= 6 and < 18, something like the below.
SET NOCOUNT OFF
SET ROWCOUNT 0
DECLARE @StartDate DateTime
DECLARE @EndDate DateTime
SET @StartDate = DATEADD(d, DATEDIFF(d, 0, DATEADD(m, -1, DATEADD(d, 1 - day(getdate()), getdate()))), 0)
SET @EndDate = DATEADD(ms, -2,DATEADD(d, DATEDIFF(d, 0, DATEADD(d, 1 - day(getdate()), getdate())), 0))
SELECT Interfaces.InterfaceId,
Nodes.NodeID,
Nodes.Caption AS NodeName,
Nodes.VendorIcon AS Vendor_Icon,
Interfaces.Caption AS Interface_Caption,
Interfaces.InterfaceIcon AS Interface_Icon,
Maxbps_In95,
Maxbps_Out95,
Maxbps_95,
Interfaces.InterfaceSpeed AS Interface_Speed,
Recieve_Percentage = (Maxbps_In95 / Interfaces.InterfaceSpeed ) * 100,
Transmit_Percentage = (Maxbps_Out95 / Interfaces.InterfaceSpeed) * 100
FROM Nodes
INNER JOIN Interfaces ON Nodes.NodeID = Interfaces.NodeID
INNER JOIN (
SELECT InterfaceID,
dbo.GetInBps95th(InterfaceID, @StartDate, @EndDate) AS Maxbps_In95,
dbo.GetOutBps95th(InterfaceID, @StartDate, @EndDate) AS Maxbps_Out95,
dbo.GetMaxBps95th(InterfaceID, @StartDate, @EndDate) AS Maxbps_95
FROM InterfaceTraffic
WHERE InterfaceTraffic.DateTime >= @StartDate AND InterfaceTraffic.DateTime <= @EndDate AND CONVERT (time, InterfaceTraffic.DateTime) >= '06:00:00' AND CONVERT(time, InterfaceTraffic.DateTime) < '18:00:00'
GROUP BY InterfaceID
) TrafficStat
ON Interfaces.InterfaceID = TrafficStat.InterfaceID
WHERE (1=1) AND
( (Nodes.TBU = 'TBU') AND (Interfaces.Link_Type LIKE '%Primary%') )