Sounds like it may be 'hot foot', especially if this has developed with longer rides and more intensive use. The cause, if so, is the shoe sole flexing around the spd mount point which in turn causes pain that feels as if it is deep within your foot bones across the full width by the ball of your foot (I speak from experience

).
If it is hot foot, the only cure if you want to stick with spds is a new pair of shoes with stiffer soles. The pain takes a few weeks to go away completely but cycling is possible from day 1 of new shoes. Some shoes have deep tread either side of the cleat position that in combination with some spd pedals acts to increase the effective width of the contact point.
Spd-sl and similar fittings have broad contact points nowhere near as prone to this problem but then they are not much good for walking around in.